Starting phenix.real_space_refine on Sun Aug 24 14:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5b_27909/08_2025/8e5b_27909.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13098 2.51 5 N 3351 2.21 5 O 3743 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20310 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'BBI': 1, 'WG6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.20 Number of scatterers: 20310 At special positions: 0 Unit cell: (171.556, 170.442, 183.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 112 16.00 P 1 15.00 F 1 9.00 O 3743 8.00 N 3351 7.00 C 13098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 883.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 17 sheets defined 54.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 127 through 146 removed outlier: 3.545A pdb=" N LEU A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 removed outlier: 4.054A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.578A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.996A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.917A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 293 Processing helix chain 'A' and resid 349 through 362 removed outlier: 3.550A pdb=" N THR A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.528A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 420 removed outlier: 3.759A pdb=" N LYS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 431 through 441 removed outlier: 3.914A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.598A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.685A pdb=" N THR A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.997A pdb=" N CYS A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.601A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.557A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 673 Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.658A pdb=" N VAL A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 Processing helix chain 'A' and resid 728 through 769 removed outlier: 4.269A pdb=" N PHE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 885 through 904 removed outlier: 3.757A pdb=" N THR A 889 " --> pdb=" O HIS A 885 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.643A pdb=" N ALA A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 Processing helix chain 'A' and resid 980 through 987 Processing helix chain 'A' and resid 988 through 995 Proline residue: A 991 - end of helix Processing helix chain 'A' and resid 998 through 1015 Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.575A pdb=" N MET A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 removed outlier: 3.566A pdb=" N LEU A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A1112 " --> pdb=" O TYR A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1139 removed outlier: 4.139A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1160 Processing helix chain 'A' and resid 1169 through 1181 removed outlier: 4.353A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A1179 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1180 " --> pdb=" O VAL A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1203 removed outlier: 4.740A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A1199 " --> pdb=" O GLN A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1223 Processing helix chain 'A' and resid 1230 through 1259 Processing helix chain 'A' and resid 1260 through 1265 removed outlier: 4.172A pdb=" N PHE A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1282 removed outlier: 3.534A pdb=" N ILE A1282 " --> pdb=" O ILE A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1288 removed outlier: 3.971A pdb=" N SER A1287 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A1288 " --> pdb=" O ALA A1285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1284 through 1288' Processing helix chain 'A' and resid 1315 through 1320 removed outlier: 3.523A pdb=" N ARG A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1315 through 1320' Processing helix chain 'A' and resid 1321 through 1333 removed outlier: 3.695A pdb=" N ARG A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A1333 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1350 Processing helix chain 'A' and resid 1350 through 1373 removed outlier: 4.580A pdb=" N ALA A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1415 Processing helix chain 'A' and resid 1439 through 1466 removed outlier: 3.861A pdb=" N ASN A1466 " --> pdb=" O VAL A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1478 through 1493 removed outlier: 3.643A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1491 " --> pdb=" O ARG A1487 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1512 Processing helix chain 'A' and resid 1526 through 1534 removed outlier: 3.553A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A1534 " --> pdb=" O ARG A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1558 removed outlier: 4.146A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1576 removed outlier: 3.887A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 52 removed outlier: 3.579A pdb=" N GLU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.784A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.560A pdb=" N ARG D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.522A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.220A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.876A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.615A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.592A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 431 through 438 removed outlier: 3.866A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.788A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.600A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 Processing helix chain 'D' and resid 638 through 647 removed outlier: 4.102A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 removed outlier: 6.030A pdb=" N ASP D 651 " --> pdb=" O LEU D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 678 through 688 removed outlier: 4.257A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 4.093A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 717 " --> pdb=" O ASN D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 752 removed outlier: 4.091A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP D 752 " --> pdb=" O GLY D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.822A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.556A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 825 " --> pdb=" O TRP D 821 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 826 " --> pdb=" O ILE D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 removed outlier: 3.691A pdb=" N ASN D 888 " --> pdb=" O ARG D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1047 removed outlier: 3.986A pdb=" N MET D1046 " --> pdb=" O ASN D1042 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D1047 " --> pdb=" O PRO D1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1042 through 1047' Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 120 through 134 removed outlier: 3.512A pdb=" N LEU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.584A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 246 through 263 removed outlier: 3.556A pdb=" N VAL C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.482A pdb=" N LYS C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.576A pdb=" N GLN C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 327 removed outlier: 3.729A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 360 removed outlier: 3.708A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.539A pdb=" N PHE A 302 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 332 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1043 through 1044 Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.504A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.537A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER D 493 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU D 458 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.537A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER D 493 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU D 458 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.442A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 357 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS D 356 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 385 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.278A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 658 through 661 removed outlier: 3.932A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 814 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'D' and resid 859 through 862 removed outlier: 7.249A pdb=" N ILE D 852 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 862 " --> pdb=" O CYS D 850 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS D 850 " --> pdb=" O ALA D 862 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 892 through 904 removed outlier: 4.519A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 115 through 119 Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.171A pdb=" N VAL C 181 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL C 292 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 183 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.693A pdb=" N SER C 213 " --> pdb=" O LEU C 266 " (cutoff:3.500A) 969 hydrogen bonds defined for protein. 2712 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: 4.11 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 6548 1.37 - 1.55: 14008 1.55 - 1.74: 12 1.74 - 1.92: 176 1.92 - 2.11: 2 Bond restraints: 20746 Sorted by residual: bond pdb=" C17 WG6 A2202 " pdb=" N19 WG6 A2202 " ideal model delta sigma weight residual 1.456 1.609 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C13 WG6 A2202 " pdb=" C14 WG6 A2202 " ideal model delta sigma weight residual 1.509 1.660 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" O12 WG6 A2202 " pdb=" P10 WG6 A2202 " ideal model delta sigma weight residual 1.590 1.711 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" O30 WG6 A2202 " pdb=" P10 WG6 A2202 " ideal model delta sigma weight residual 1.606 1.710 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C02 WG6 A2202 " pdb=" C03 WG6 A2202 " ideal model delta sigma weight residual 1.531 1.619 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 20741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 27695 2.03 - 4.07: 330 4.07 - 6.10: 54 6.10 - 8.13: 16 8.13 - 10.17: 9 Bond angle restraints: 28104 Sorted by residual: angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 113.53 109.37 4.16 9.80e-01 1.04e+00 1.80e+01 angle pdb=" C31 WG6 A2202 " pdb=" O30 WG6 A2202 " pdb=" P10 WG6 A2202 " ideal model delta sigma weight residual 122.37 132.54 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET A1369 " pdb=" CG MET A1369 " pdb=" SD MET A1369 " ideal model delta sigma weight residual 112.70 102.64 10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N19 WG6 A2202 " pdb=" C17 WG6 A2202 " pdb=" O18 WG6 A2202 " ideal model delta sigma weight residual 107.94 117.80 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N09 WG6 A2202 " pdb=" P10 WG6 A2202 " pdb=" O30 WG6 A2202 " ideal model delta sigma weight residual 100.07 109.44 -9.37 3.00e+00 1.11e-01 9.76e+00 ... (remaining 28099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.73: 11714 23.73 - 47.47: 773 47.47 - 71.20: 94 71.20 - 94.94: 36 94.94 - 118.67: 15 Dihedral angle restraints: 12632 sinusoidal: 5315 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 175.55 -82.55 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual 93.00 42.65 50.35 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 12629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 3195 0.184 - 0.368: 3 0.368 - 0.553: 2 0.553 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 3201 Sorted by residual: chirality pdb=" P10 WG6 A2202 " pdb=" O11 WG6 A2202 " pdb=" O12 WG6 A2202 " pdb=" O30 WG6 A2202 " both_signs ideal model delta sigma weight residual True 2.67 -3.59 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" C16 WG6 A2202 " pdb=" C15 WG6 A2202 " pdb=" C17 WG6 A2202 " pdb=" C27 WG6 A2202 " both_signs ideal model delta sigma weight residual False -2.71 -3.10 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3198 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 348 " -0.020 2.00e-02 2.50e+03 1.89e-02 4.48e+00 pdb=" CG ASN D 348 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN D 348 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN D 348 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 140 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO C 141 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 516 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO D 517 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 517 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 517 " 0.025 5.00e-02 4.00e+02 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.74: 1393 2.74 - 3.29: 21399 3.29 - 3.85: 33606 3.85 - 4.40: 40828 4.40 - 4.96: 69793 Nonbonded interactions: 167019 Sorted by model distance: nonbonded pdb=" OE2 GLU D 182 " pdb=" OG SER D 210 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR D 450 " pdb=" OG1 THR D 461 " model vdw 2.181 3.040 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.196 3.040 nonbonded pdb=" O ALA A 519 " pdb=" OG SER A 522 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 911 " pdb=" OD2 ASP A1426 " model vdw 2.234 3.040 ... (remaining 167014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.004 0.153 20770 Z= 0.200 Angle : 0.600 10.760 28166 Z= 0.289 Chirality : 0.047 0.921 3201 Planarity : 0.003 0.052 3555 Dihedral : 16.131 118.669 7866 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: -0.27 (0.17), residues: 2472 helix: 0.69 (0.15), residues: 1172 sheet: -0.07 (0.33), residues: 270 loop : -1.18 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1378 TYR 0.013 0.001 TYR A1443 PHE 0.020 0.001 PHE A1343 TRP 0.022 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00433 (20746) covalent geometry : angle 0.58611 (28104) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.65121 ( 20) hydrogen bonds : bond 0.22122 ( 956) hydrogen bonds : angle 6.66622 ( 2712) link_BETA1-4 : bond 0.00840 ( 8) link_BETA1-4 : angle 2.42024 ( 24) link_NAG-ASN : bond 0.00865 ( 6) link_NAG-ASN : angle 3.94962 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 730 ILE cc_start: 0.8839 (pt) cc_final: 0.8602 (pt) REVERT: D 268 THR cc_start: 0.9342 (t) cc_final: 0.9033 (m) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1183 time to fit residues: 53.2712 Evaluate side-chains 224 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0170 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 555 GLN A1381 ASN D 422 ASN D 682 ASN D 713 ASN D 753 GLN ** D 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136553 restraints weight = 25635.228| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.52 r_work: 0.3048 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20770 Z= 0.130 Angle : 0.584 12.265 28166 Z= 0.291 Chirality : 0.043 0.249 3201 Planarity : 0.004 0.050 3555 Dihedral : 9.911 105.692 3051 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.59 % Allowed : 6.79 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.03 (0.17), residues: 2472 helix: 1.01 (0.15), residues: 1204 sheet: -0.21 (0.33), residues: 270 loop : -1.11 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.022 0.001 TYR D 719 PHE 0.018 0.001 PHE A 202 TRP 0.016 0.001 TRP A1199 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00282 (20746) covalent geometry : angle 0.57049 (28104) SS BOND : bond 0.00269 ( 10) SS BOND : angle 1.18991 ( 20) hydrogen bonds : bond 0.04873 ( 956) hydrogen bonds : angle 4.68795 ( 2712) link_BETA1-4 : bond 0.00900 ( 8) link_BETA1-4 : angle 2.20631 ( 24) link_NAG-ASN : bond 0.00916 ( 6) link_NAG-ASN : angle 4.24990 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6728 (mp) REVERT: A 311 GLU cc_start: 0.7921 (pm20) cc_final: 0.7288 (pt0) REVERT: A 727 ILE cc_start: 0.9153 (tp) cc_final: 0.8890 (tp) REVERT: A 760 SER cc_start: 0.8886 (t) cc_final: 0.8652 (t) REVERT: A 1164 LYS cc_start: 0.5523 (mptt) cc_final: 0.5128 (mtpt) REVERT: A 1278 ILE cc_start: 0.7996 (mm) cc_final: 0.7739 (mm) REVERT: A 1344 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8931 (mp) REVERT: D 41 GLN cc_start: 0.8108 (pp30) cc_final: 0.7115 (pp30) REVERT: D 77 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: D 149 PHE cc_start: 0.8822 (m-10) cc_final: 0.8572 (m-10) REVERT: D 182 GLU cc_start: 0.8751 (tp30) cc_final: 0.8535 (tp30) outliers start: 13 outliers final: 8 residues processed: 261 average time/residue: 0.1261 time to fit residues: 53.8377 Evaluate side-chains 244 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 233 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 1045 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 207 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 161 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN D 869 ASN ** D 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136232 restraints weight = 26038.852| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.26 r_work: 0.3035 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20770 Z= 0.111 Angle : 0.542 11.890 28166 Z= 0.267 Chirality : 0.042 0.255 3201 Planarity : 0.003 0.050 3555 Dihedral : 8.451 101.584 3051 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.22 % Allowed : 9.91 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.17 (0.17), residues: 2472 helix: 1.19 (0.15), residues: 1205 sheet: -0.28 (0.32), residues: 274 loop : -1.10 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.011 0.001 TYR D 719 PHE 0.016 0.001 PHE D 588 TRP 0.020 0.001 TRP D 752 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00245 (20746) covalent geometry : angle 0.52807 (28104) SS BOND : bond 0.00303 ( 10) SS BOND : angle 1.13337 ( 20) hydrogen bonds : bond 0.03985 ( 956) hydrogen bonds : angle 4.35926 ( 2712) link_BETA1-4 : bond 0.00747 ( 8) link_BETA1-4 : angle 2.24060 ( 24) link_NAG-ASN : bond 0.00771 ( 6) link_NAG-ASN : angle 4.08859 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.808 Fit side-chains REVERT: A 130 ILE cc_start: 0.7353 (tt) cc_final: 0.6991 (pt) REVERT: A 170 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6640 (mp) REVERT: A 254 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7826 (m) REVERT: A 311 GLU cc_start: 0.7876 (pm20) cc_final: 0.7213 (pt0) REVERT: A 760 SER cc_start: 0.8863 (t) cc_final: 0.8583 (t) REVERT: A 1150 PHE cc_start: 0.8359 (t80) cc_final: 0.8141 (t80) REVERT: A 1164 LYS cc_start: 0.5471 (mptt) cc_final: 0.5125 (mtpt) REVERT: A 1344 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 77 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: D 149 PHE cc_start: 0.8780 (m-10) cc_final: 0.8519 (m-10) REVERT: D 268 THR cc_start: 0.9283 (t) cc_final: 0.9002 (m) REVERT: D 495 GLU cc_start: 0.8084 (mp0) cc_final: 0.7818 (mm-30) REVERT: D 994 LEU cc_start: 0.8250 (tp) cc_final: 0.8040 (tp) REVERT: C 196 MET cc_start: 0.6424 (tmm) cc_final: 0.6122 (tpt) outliers start: 27 outliers final: 15 residues processed: 272 average time/residue: 0.1190 time to fit residues: 52.6430 Evaluate side-chains 257 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 34 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A1017 ASN A1114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133452 restraints weight = 25867.945| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.72 r_work: 0.3078 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20770 Z= 0.165 Angle : 0.580 11.592 28166 Z= 0.286 Chirality : 0.043 0.259 3201 Planarity : 0.004 0.050 3555 Dihedral : 7.898 96.572 3051 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.90 % Allowed : 11.67 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.05 (0.17), residues: 2472 helix: 1.14 (0.15), residues: 1211 sheet: -0.39 (0.32), residues: 275 loop : -1.22 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1472 TYR 0.013 0.001 TYR D1068 PHE 0.015 0.001 PHE A 293 TRP 0.013 0.001 TRP A1103 HIS 0.004 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00399 (20746) covalent geometry : angle 0.56549 (28104) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.59689 ( 20) hydrogen bonds : bond 0.04083 ( 956) hydrogen bonds : angle 4.29477 ( 2712) link_BETA1-4 : bond 0.00814 ( 8) link_BETA1-4 : angle 2.39641 ( 24) link_NAG-ASN : bond 0.00713 ( 6) link_NAG-ASN : angle 4.03961 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7371 (tt) cc_final: 0.7088 (pt) REVERT: A 170 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6804 (mp) REVERT: A 293 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.6737 (p90) REVERT: A 582 TYR cc_start: 0.7170 (m-80) cc_final: 0.6874 (m-80) REVERT: A 1150 PHE cc_start: 0.8278 (t80) cc_final: 0.8072 (t80) REVERT: A 1164 LYS cc_start: 0.5451 (mptt) cc_final: 0.4725 (mmtt) REVERT: A 1344 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8973 (mp) REVERT: D 77 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: D 268 THR cc_start: 0.9347 (t) cc_final: 0.9031 (m) REVERT: D 859 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8429 (tp) outliers start: 42 outliers final: 29 residues processed: 265 average time/residue: 0.1121 time to fit residues: 49.2648 Evaluate side-chains 264 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A1114 ASN D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133157 restraints weight = 25716.089| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.69 r_work: 0.3021 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20770 Z= 0.248 Angle : 0.654 11.727 28166 Z= 0.324 Chirality : 0.046 0.294 3201 Planarity : 0.004 0.050 3555 Dihedral : 7.853 89.987 3051 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.44 % Allowed : 13.35 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: -0.21 (0.17), residues: 2472 helix: 0.93 (0.15), residues: 1216 sheet: -0.56 (0.31), residues: 277 loop : -1.36 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1472 TYR 0.017 0.002 TYR D1068 PHE 0.020 0.002 PHE A1147 TRP 0.015 0.002 TRP A1103 HIS 0.005 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00608 (20746) covalent geometry : angle 0.63813 (28104) SS BOND : bond 0.00415 ( 10) SS BOND : angle 1.93297 ( 20) hydrogen bonds : bond 0.04565 ( 956) hydrogen bonds : angle 4.42131 ( 2712) link_BETA1-4 : bond 0.00877 ( 8) link_BETA1-4 : angle 2.67481 ( 24) link_NAG-ASN : bond 0.00729 ( 6) link_NAG-ASN : angle 4.36003 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7487 (tt) cc_final: 0.7209 (pt) REVERT: A 170 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6663 (mp) REVERT: A 202 PHE cc_start: 0.7591 (p90) cc_final: 0.7139 (p90) REVERT: A 293 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.7161 (p90) REVERT: A 582 TYR cc_start: 0.7357 (m-80) cc_final: 0.7012 (m-80) REVERT: A 1114 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (m-40) REVERT: A 1150 PHE cc_start: 0.8405 (t80) cc_final: 0.8189 (t80) REVERT: A 1164 LYS cc_start: 0.5567 (mptt) cc_final: 0.4763 (mmtt) REVERT: A 1344 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9044 (mp) REVERT: D 268 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9075 (m) REVERT: D 506 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8954 (mt) REVERT: D 859 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8545 (tp) REVERT: D 1009 MET cc_start: 0.8605 (tpt) cc_final: 0.8346 (tpt) outliers start: 54 outliers final: 35 residues processed: 277 average time/residue: 0.1118 time to fit residues: 50.6973 Evaluate side-chains 271 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 109 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136441 restraints weight = 25533.220| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.67 r_work: 0.3085 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20770 Z= 0.111 Angle : 0.555 11.727 28166 Z= 0.273 Chirality : 0.042 0.269 3201 Planarity : 0.004 0.047 3555 Dihedral : 7.340 86.784 3051 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.49 % Allowed : 15.20 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.03 (0.17), residues: 2472 helix: 1.18 (0.15), residues: 1219 sheet: -0.54 (0.32), residues: 275 loop : -1.28 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1472 TYR 0.013 0.001 TYR D 644 PHE 0.015 0.001 PHE A1147 TRP 0.028 0.001 TRP A 441 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00249 (20746) covalent geometry : angle 0.53916 (28104) SS BOND : bond 0.00363 ( 10) SS BOND : angle 1.29036 ( 20) hydrogen bonds : bond 0.03555 ( 956) hydrogen bonds : angle 4.16287 ( 2712) link_BETA1-4 : bond 0.00764 ( 8) link_BETA1-4 : angle 2.52039 ( 24) link_NAG-ASN : bond 0.00768 ( 6) link_NAG-ASN : angle 4.14893 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7486 (tt) cc_final: 0.7230 (pt) REVERT: A 170 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6732 (mp) REVERT: A 202 PHE cc_start: 0.7574 (p90) cc_final: 0.7152 (p90) REVERT: A 293 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 570 MET cc_start: 0.6678 (tpt) cc_final: 0.6410 (tpt) REVERT: A 582 TYR cc_start: 0.7233 (m-80) cc_final: 0.6906 (m-80) REVERT: A 1150 PHE cc_start: 0.8307 (t80) cc_final: 0.8065 (t80) REVERT: A 1164 LYS cc_start: 0.5473 (mptt) cc_final: 0.4761 (mmtt) REVERT: A 1344 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (mp) REVERT: D 268 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9047 (m) REVERT: D 506 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9063 (mt) REVERT: D 859 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8503 (tp) REVERT: D 889 ILE cc_start: 0.8490 (mm) cc_final: 0.8204 (tp) REVERT: D 1009 MET cc_start: 0.8592 (tpt) cc_final: 0.8331 (tpt) outliers start: 33 outliers final: 19 residues processed: 267 average time/residue: 0.1171 time to fit residues: 51.7744 Evaluate side-chains 255 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 972 GLN Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 182 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 231 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134261 restraints weight = 25669.883| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.76 r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20770 Z= 0.114 Angle : 0.551 11.468 28166 Z= 0.270 Chirality : 0.042 0.276 3201 Planarity : 0.003 0.047 3555 Dihedral : 7.098 82.486 3051 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.99 % Allowed : 15.34 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.03 (0.17), residues: 2472 helix: 1.20 (0.15), residues: 1227 sheet: -0.57 (0.32), residues: 275 loop : -1.32 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1472 TYR 0.012 0.001 TYR D 644 PHE 0.013 0.001 PHE A1147 TRP 0.016 0.001 TRP A 441 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00264 (20746) covalent geometry : angle 0.53477 (28104) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.34442 ( 20) hydrogen bonds : bond 0.03472 ( 956) hydrogen bonds : angle 4.11753 ( 2712) link_BETA1-4 : bond 0.00740 ( 8) link_BETA1-4 : angle 2.57675 ( 24) link_NAG-ASN : bond 0.00706 ( 6) link_NAG-ASN : angle 4.12189 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7447 (tt) cc_final: 0.7217 (pt) REVERT: A 170 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6774 (mp) REVERT: A 202 PHE cc_start: 0.7607 (p90) cc_final: 0.7271 (p90) REVERT: A 293 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7014 (p90) REVERT: A 570 MET cc_start: 0.6711 (tpt) cc_final: 0.6472 (tpt) REVERT: A 582 TYR cc_start: 0.7206 (m-80) cc_final: 0.6855 (m-80) REVERT: A 616 SER cc_start: 0.8253 (t) cc_final: 0.8013 (m) REVERT: A 1114 ASN cc_start: 0.8545 (m-40) cc_final: 0.8336 (t0) REVERT: A 1164 LYS cc_start: 0.5476 (mptt) cc_final: 0.4761 (mmtt) REVERT: A 1344 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9006 (mp) REVERT: D 77 GLN cc_start: 0.8597 (tp40) cc_final: 0.8200 (mp10) REVERT: D 268 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9026 (m) REVERT: D 495 GLU cc_start: 0.8062 (mp0) cc_final: 0.7721 (mm-30) REVERT: D 506 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9013 (mt) REVERT: D 859 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8550 (tp) REVERT: D 861 MET cc_start: 0.7558 (ptm) cc_final: 0.7342 (ptm) REVERT: D 879 ASP cc_start: 0.8073 (t0) cc_final: 0.7812 (t0) REVERT: D 889 ILE cc_start: 0.8555 (mm) cc_final: 0.8313 (tp) REVERT: D 895 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8469 (m110) REVERT: D 1009 MET cc_start: 0.8564 (tpt) cc_final: 0.8305 (tpt) REVERT: C 196 MET cc_start: 0.7087 (mmt) cc_final: 0.6840 (tpp) outliers start: 44 outliers final: 24 residues processed: 270 average time/residue: 0.1284 time to fit residues: 56.9870 Evaluate side-chains 264 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 174 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 237 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 151 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 0.3980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN A1394 GLN ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137106 restraints weight = 25400.318| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.41 r_work: 0.3087 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 20770 Z= 0.097 Angle : 0.531 11.121 28166 Z= 0.259 Chirality : 0.041 0.291 3201 Planarity : 0.003 0.046 3555 Dihedral : 6.574 73.102 3051 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.67 % Allowed : 15.97 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.20 (0.17), residues: 2472 helix: 1.38 (0.15), residues: 1206 sheet: -0.51 (0.32), residues: 271 loop : -1.25 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1472 TYR 0.013 0.001 TYR D 644 PHE 0.023 0.001 PHE A1150 TRP 0.013 0.001 TRP A 441 HIS 0.002 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00214 (20746) covalent geometry : angle 0.51575 (28104) SS BOND : bond 0.00250 ( 10) SS BOND : angle 1.04509 ( 20) hydrogen bonds : bond 0.03060 ( 956) hydrogen bonds : angle 3.98722 ( 2712) link_BETA1-4 : bond 0.00707 ( 8) link_BETA1-4 : angle 2.68159 ( 24) link_NAG-ASN : bond 0.00743 ( 6) link_NAG-ASN : angle 3.91701 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7351 (tt) cc_final: 0.7100 (pt) REVERT: A 170 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6745 (mp) REVERT: A 202 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7384 (p90) REVERT: A 293 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.6768 (p90) REVERT: A 570 MET cc_start: 0.6812 (tpt) cc_final: 0.6584 (tpt) REVERT: A 582 TYR cc_start: 0.7379 (m-80) cc_final: 0.6959 (m-80) REVERT: A 616 SER cc_start: 0.8313 (t) cc_final: 0.8066 (m) REVERT: A 1164 LYS cc_start: 0.5529 (mptt) cc_final: 0.4850 (mmtt) REVERT: A 1344 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8947 (mp) REVERT: D 77 GLN cc_start: 0.8752 (tp40) cc_final: 0.8274 (mp10) REVERT: D 149 PHE cc_start: 0.8755 (m-10) cc_final: 0.8495 (m-10) REVERT: D 268 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9081 (m) REVERT: D 405 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7541 (tm-30) REVERT: D 506 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (mt) REVERT: D 859 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8605 (tp) REVERT: D 879 ASP cc_start: 0.8325 (t0) cc_final: 0.7958 (t0) REVERT: D 1009 MET cc_start: 0.8719 (tpt) cc_final: 0.8495 (tpt) REVERT: C 196 MET cc_start: 0.7143 (mmt) cc_final: 0.6808 (tpp) outliers start: 37 outliers final: 25 residues processed: 273 average time/residue: 0.1245 time to fit residues: 55.7601 Evaluate side-chains 270 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 191 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 228 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A 677 ASN A1114 ASN A1381 ASN ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135259 restraints weight = 25482.439| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.62 r_work: 0.3078 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20770 Z= 0.167 Angle : 0.593 11.235 28166 Z= 0.292 Chirality : 0.043 0.284 3201 Planarity : 0.004 0.048 3555 Dihedral : 6.548 61.569 3051 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.81 % Allowed : 16.20 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.06 (0.17), residues: 2472 helix: 1.29 (0.15), residues: 1219 sheet: -0.65 (0.31), residues: 277 loop : -1.35 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 197 TYR 0.013 0.001 TYR A1122 PHE 0.016 0.001 PHE A 688 TRP 0.023 0.001 TRP A 441 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00408 (20746) covalent geometry : angle 0.57702 (28104) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.65830 ( 20) hydrogen bonds : bond 0.03687 ( 956) hydrogen bonds : angle 4.11769 ( 2712) link_BETA1-4 : bond 0.00666 ( 8) link_BETA1-4 : angle 2.90824 ( 24) link_NAG-ASN : bond 0.00697 ( 6) link_NAG-ASN : angle 3.95143 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7315 (tt) cc_final: 0.7114 (pt) REVERT: A 170 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6622 (mp) REVERT: A 202 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7473 (p90) REVERT: A 293 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.6896 (p90) REVERT: A 570 MET cc_start: 0.6731 (tpt) cc_final: 0.6494 (tpt) REVERT: A 582 TYR cc_start: 0.7080 (m-80) cc_final: 0.6688 (m-80) REVERT: A 616 SER cc_start: 0.8355 (t) cc_final: 0.8117 (m) REVERT: A 741 TYR cc_start: 0.8972 (t80) cc_final: 0.8758 (t80) REVERT: A 1164 LYS cc_start: 0.5505 (mptt) cc_final: 0.4781 (mmtt) REVERT: A 1344 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8969 (mp) REVERT: D 77 GLN cc_start: 0.8611 (tp40) cc_final: 0.8180 (mp10) REVERT: D 268 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9019 (m) REVERT: D 506 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9009 (mt) REVERT: D 859 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8525 (tp) REVERT: D 879 ASP cc_start: 0.8217 (t0) cc_final: 0.7895 (t0) REVERT: D 1009 MET cc_start: 0.8541 (tpt) cc_final: 0.8296 (tpt) outliers start: 40 outliers final: 29 residues processed: 261 average time/residue: 0.1323 time to fit residues: 56.2860 Evaluate side-chains 270 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 32 optimal weight: 0.0060 chunk 68 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134337 restraints weight = 25565.988| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.69 r_work: 0.3084 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20770 Z= 0.125 Angle : 0.733 59.118 28166 Z= 0.392 Chirality : 0.042 0.283 3201 Planarity : 0.004 0.048 3555 Dihedral : 6.556 61.462 3051 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.58 % Allowed : 16.79 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.08 (0.17), residues: 2472 helix: 1.33 (0.15), residues: 1214 sheet: -0.66 (0.31), residues: 277 loop : -1.36 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 197 TYR 0.014 0.001 TYR D 161 PHE 0.016 0.001 PHE A1447 TRP 0.027 0.001 TRP A 441 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00286 (20746) covalent geometry : angle 0.72141 (28104) SS BOND : bond 0.00251 ( 10) SS BOND : angle 1.58853 ( 20) hydrogen bonds : bond 0.03561 ( 956) hydrogen bonds : angle 4.11640 ( 2712) link_BETA1-4 : bond 0.00659 ( 8) link_BETA1-4 : angle 2.87780 ( 24) link_NAG-ASN : bond 0.00701 ( 6) link_NAG-ASN : angle 3.92744 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7275 (tt) cc_final: 0.7072 (pt) REVERT: A 170 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 202 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7465 (p90) REVERT: A 293 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.6956 (p90) REVERT: A 570 MET cc_start: 0.6793 (tpt) cc_final: 0.6555 (tpt) REVERT: A 582 TYR cc_start: 0.7072 (m-80) cc_final: 0.6668 (m-80) REVERT: A 616 SER cc_start: 0.8345 (t) cc_final: 0.8099 (m) REVERT: A 741 TYR cc_start: 0.8958 (t80) cc_final: 0.8751 (t80) REVERT: A 1164 LYS cc_start: 0.5461 (mptt) cc_final: 0.4766 (mmtt) REVERT: A 1344 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8955 (mp) REVERT: D 77 GLN cc_start: 0.8608 (tp40) cc_final: 0.8176 (mp10) REVERT: D 268 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9010 (m) REVERT: D 506 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8999 (mt) REVERT: D 859 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8524 (tp) REVERT: D 879 ASP cc_start: 0.8230 (t0) cc_final: 0.7881 (t0) REVERT: D 1009 MET cc_start: 0.8537 (tpt) cc_final: 0.8296 (tpt) REVERT: C 196 MET cc_start: 0.6651 (mmm) cc_final: 0.6297 (mmt) outliers start: 35 outliers final: 27 residues processed: 256 average time/residue: 0.1353 time to fit residues: 56.7695 Evaluate side-chains 268 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 234 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134607 restraints weight = 25575.763| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.68 r_work: 0.3080 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20770 Z= 0.125 Angle : 0.733 59.117 28166 Z= 0.392 Chirality : 0.042 0.283 3201 Planarity : 0.004 0.048 3555 Dihedral : 6.556 61.462 3051 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.54 % Allowed : 16.92 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.08 (0.17), residues: 2472 helix: 1.33 (0.15), residues: 1214 sheet: -0.66 (0.31), residues: 277 loop : -1.36 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 197 TYR 0.014 0.001 TYR D 161 PHE 0.016 0.001 PHE A1447 TRP 0.027 0.001 TRP A 441 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00286 (20746) covalent geometry : angle 0.72141 (28104) SS BOND : bond 0.00251 ( 10) SS BOND : angle 1.58853 ( 20) hydrogen bonds : bond 0.03561 ( 956) hydrogen bonds : angle 4.11640 ( 2712) link_BETA1-4 : bond 0.00659 ( 8) link_BETA1-4 : angle 2.87779 ( 24) link_NAG-ASN : bond 0.00701 ( 6) link_NAG-ASN : angle 3.92744 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5770.76 seconds wall clock time: 99 minutes 7.87 seconds (5947.87 seconds total)