Starting phenix.real_space_refine on Wed Jun 18 01:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5b_27909/06_2025/8e5b_27909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5b_27909/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5b_27909/06_2025/8e5b_27909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5b_27909/06_2025/8e5b_27909.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5b_27909/06_2025/8e5b_27909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5b_27909/06_2025/8e5b_27909.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.01, per 1000 atoms: 0.54 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: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.45 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: 8.41 Time building geometry restraints manager: 6.00 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 47.020 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- 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 : 6.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.022 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 PHE 0.020 0.001 PHE A1343 TYR 0.013 0.001 TYR A1443 ARG 0.003 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 6) link_NAG-ASN : angle 3.94962 ( 18) link_BETA1-4 : bond 0.00840 ( 8) link_BETA1-4 : angle 2.42024 ( 24) hydrogen bonds : bond 0.22122 ( 956) hydrogen bonds : angle 6.66622 ( 2712) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.65121 ( 20) covalent geometry : bond 0.00433 (20746) covalent geometry : angle 0.58611 (28104) *********************** 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 : 2.243 Fit side-chains 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: 0.2860 time to fit residues: 127.5294 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 : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 118 optimal weight: 20.0000 chunk 145 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.176881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136817 restraints weight = 25463.422| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.47 r_work: 0.3069 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20770 Z= 0.135 Angle : 0.587 12.209 28166 Z= 0.292 Chirality : 0.043 0.257 3201 Planarity : 0.004 0.050 3555 Dihedral : 9.992 105.788 3051 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.63 % Allowed : 6.97 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2472 helix: 0.99 (0.15), residues: 1204 sheet: -0.22 (0.33), residues: 270 loop : -1.12 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1199 HIS 0.005 0.001 HIS C 94 PHE 0.019 0.001 PHE A 202 TYR 0.022 0.001 TYR D 719 ARG 0.002 0.000 ARG A 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00860 ( 6) link_NAG-ASN : angle 4.24725 ( 18) link_BETA1-4 : bond 0.00747 ( 8) link_BETA1-4 : angle 2.23077 ( 24) hydrogen bonds : bond 0.05070 ( 956) hydrogen bonds : angle 4.71334 ( 2712) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.24964 ( 20) covalent geometry : bond 0.00301 (20746) covalent geometry : angle 0.57315 (28104) *********************** 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 266 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 2.085 Fit side-chains REVERT: A 170 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6832 (mp) REVERT: A 311 GLU cc_start: 0.7985 (pm20) cc_final: 0.7352 (pt0) REVERT: A 727 ILE cc_start: 0.9055 (tp) cc_final: 0.8820 (tp) REVERT: A 753 ASP cc_start: 0.7325 (m-30) cc_final: 0.7103 (m-30) REVERT: A 760 SER cc_start: 0.8990 (t) cc_final: 0.8777 (t) REVERT: A 934 ILE cc_start: 0.8185 (pt) cc_final: 0.7964 (mt) REVERT: A 1164 LYS cc_start: 0.5488 (mptt) cc_final: 0.5112 (mtpt) REVERT: A 1278 ILE cc_start: 0.8007 (mm) cc_final: 0.7753 (mm) REVERT: A 1344 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8945 (mp) REVERT: D 77 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: D 149 PHE cc_start: 0.8757 (m-10) cc_final: 0.8535 (m-10) REVERT: D 719 TYR cc_start: 0.8173 (t80) cc_final: 0.7881 (t80) REVERT: D 859 LEU cc_start: 0.8658 (tt) cc_final: 0.8429 (tp) outliers start: 14 outliers final: 9 residues processed: 259 average time/residue: 0.3185 time to fit residues: 136.6316 Evaluate side-chains 239 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 798 VAL 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 244 optimal weight: 10.0000 chunk 235 optimal weight: 0.0060 chunk 116 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 201 optimal weight: 9.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.179039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137861 restraints weight = 25686.089| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.60 r_work: 0.3068 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20770 Z= 0.104 Angle : 0.538 11.966 28166 Z= 0.264 Chirality : 0.042 0.250 3201 Planarity : 0.003 0.050 3555 Dihedral : 8.541 102.065 3051 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.09 % Allowed : 10.23 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2472 helix: 1.20 (0.15), residues: 1204 sheet: -0.29 (0.32), residues: 275 loop : -1.11 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1199 HIS 0.003 0.000 HIS C 94 PHE 0.015 0.001 PHE A 202 TYR 0.012 0.001 TYR D 719 ARG 0.003 0.000 ARG A 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 6) link_NAG-ASN : angle 4.08813 ( 18) link_BETA1-4 : bond 0.00762 ( 8) link_BETA1-4 : angle 2.23038 ( 24) hydrogen bonds : bond 0.03911 ( 956) hydrogen bonds : angle 4.35866 ( 2712) SS BOND : bond 0.00265 ( 10) SS BOND : angle 1.03272 ( 20) covalent geometry : bond 0.00218 (20746) covalent geometry : angle 0.52371 (28104) *********************** 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 284 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 3.736 Fit side-chains REVERT: A 130 ILE cc_start: 0.7448 (tt) cc_final: 0.7113 (pt) REVERT: A 170 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6555 (mp) REVERT: A 254 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7913 (m) REVERT: A 311 GLU cc_start: 0.7897 (pm20) cc_final: 0.7260 (pt0) REVERT: A 582 TYR cc_start: 0.7213 (m-80) cc_final: 0.6957 (m-80) REVERT: A 727 ILE cc_start: 0.9099 (tp) cc_final: 0.8849 (tp) REVERT: A 1164 LYS cc_start: 0.5432 (mptt) cc_final: 0.5098 (mtpt) REVERT: A 1344 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (mp) REVERT: D 77 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: D 149 PHE cc_start: 0.8681 (m-10) cc_final: 0.8438 (m-10) REVERT: D 859 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 196 MET cc_start: 0.6285 (tmm) cc_final: 0.6065 (tpt) outliers start: 24 outliers final: 12 residues processed: 272 average time/residue: 0.5512 time to fit residues: 244.5821 Evaluate side-chains 255 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 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 359 MET Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU 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 203 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 220 optimal weight: 30.0000 chunk 131 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134046 restraints weight = 24789.663| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.10 r_work: 0.3082 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20770 Z= 0.143 Angle : 0.563 11.508 28166 Z= 0.277 Chirality : 0.043 0.260 3201 Planarity : 0.004 0.049 3555 Dihedral : 7.842 97.367 3051 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.76 % Allowed : 11.54 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2472 helix: 1.17 (0.15), residues: 1206 sheet: -0.36 (0.32), residues: 275 loop : -1.17 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.003 0.001 HIS A 544 PHE 0.015 0.001 PHE D 733 TYR 0.012 0.001 TYR D1068 ARG 0.006 0.000 ARG A1472 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 6) link_NAG-ASN : angle 3.99698 ( 18) link_BETA1-4 : bond 0.00790 ( 8) link_BETA1-4 : angle 2.37099 ( 24) hydrogen bonds : bond 0.03901 ( 956) hydrogen bonds : angle 4.24444 ( 2712) SS BOND : bond 0.00300 ( 10) SS BOND : angle 1.45595 ( 20) covalent geometry : bond 0.00342 (20746) covalent geometry : angle 0.54858 (28104) *********************** 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 283 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 2.203 Fit side-chains REVERT: A 130 ILE cc_start: 0.7436 (tt) cc_final: 0.7126 (pt) REVERT: A 170 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6866 (mp) REVERT: A 202 PHE cc_start: 0.7310 (p90) cc_final: 0.7053 (p90) REVERT: A 293 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.6721 (p90) REVERT: A 582 TYR cc_start: 0.7256 (m-80) cc_final: 0.6979 (m-80) REVERT: A 1150 PHE cc_start: 0.8375 (t80) cc_final: 0.8160 (t80) REVERT: A 1164 LYS cc_start: 0.5533 (mptt) cc_final: 0.4765 (mmtt) REVERT: A 1344 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8991 (mp) REVERT: D 77 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: D 80 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8040 (mt-10) REVERT: D 268 THR cc_start: 0.9364 (t) cc_final: 0.9053 (m) REVERT: D 859 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8459 (tp) REVERT: D 861 MET cc_start: 0.7812 (ppp) cc_final: 0.7604 (ptm) outliers start: 39 outliers final: 26 residues processed: 265 average time/residue: 0.2851 time to fit residues: 123.3617 Evaluate side-chains 259 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 621 VAL Chi-restraints excluded: chain A residue 898 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 625 THR 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 1045 ASP 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 61 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 169 optimal weight: 0.0070 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN C 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.176220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135307 restraints weight = 25587.856| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.57 r_work: 0.3072 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20770 Z= 0.145 Angle : 0.564 11.481 28166 Z= 0.276 Chirality : 0.043 0.261 3201 Planarity : 0.003 0.051 3555 Dihedral : 7.546 93.124 3051 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.72 % Allowed : 13.57 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2472 helix: 1.19 (0.15), residues: 1212 sheet: -0.43 (0.32), residues: 275 loop : -1.22 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 441 HIS 0.003 0.001 HIS A 544 PHE 0.014 0.001 PHE A1147 TYR 0.011 0.001 TYR D1068 ARG 0.004 0.000 ARG A1472 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 6) link_NAG-ASN : angle 4.15866 ( 18) link_BETA1-4 : bond 0.00796 ( 8) link_BETA1-4 : angle 2.46552 ( 24) hydrogen bonds : bond 0.03753 ( 956) hydrogen bonds : angle 4.20070 ( 2712) SS BOND : bond 0.00279 ( 10) SS BOND : angle 1.35027 ( 20) covalent geometry : bond 0.00347 (20746) covalent geometry : angle 0.54858 (28104) *********************** 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 281 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 2.334 Fit side-chains REVERT: A 130 ILE cc_start: 0.7370 (tt) cc_final: 0.7116 (pt) REVERT: A 170 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6857 (mp) REVERT: A 202 PHE cc_start: 0.7437 (p90) cc_final: 0.7127 (p90) REVERT: A 293 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.6895 (p90) REVERT: A 582 TYR cc_start: 0.7213 (m-80) cc_final: 0.6892 (m-80) REVERT: A 1150 PHE cc_start: 0.8268 (t80) cc_final: 0.8066 (t80) REVERT: A 1164 LYS cc_start: 0.5490 (mptt) cc_final: 0.4754 (mmtt) REVERT: A 1344 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 77 GLN cc_start: 0.8556 (tp40) cc_final: 0.8143 (mp10) REVERT: D 80 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7801 (mt-10) REVERT: D 268 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9020 (m) REVERT: D 506 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9043 (mt) REVERT: D 719 TYR cc_start: 0.8009 (t80) cc_final: 0.7774 (t80) REVERT: D 879 ASP cc_start: 0.7974 (t70) cc_final: 0.7737 (t0) outliers start: 38 outliers final: 26 residues processed: 263 average time/residue: 0.2841 time to fit residues: 124.2736 Evaluate side-chains 260 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 616 SER Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 760 SER 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 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 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 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 100 optimal weight: 0.8980 chunk 169 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN D 108 GLN D 972 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138037 restraints weight = 25830.155| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.65 r_work: 0.3093 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 20770 Z= 0.101 Angle : 0.527 11.086 28166 Z= 0.257 Chirality : 0.041 0.273 3201 Planarity : 0.003 0.048 3555 Dihedral : 7.136 88.848 3051 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 14.12 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2472 helix: 1.30 (0.15), residues: 1213 sheet: -0.45 (0.32), residues: 275 loop : -1.28 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.002 0.000 HIS C 94 PHE 0.012 0.001 PHE A1147 TYR 0.011 0.001 TYR D 644 ARG 0.004 0.000 ARG A1472 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 6) link_NAG-ASN : angle 4.04027 ( 18) link_BETA1-4 : bond 0.00739 ( 8) link_BETA1-4 : angle 2.43795 ( 24) hydrogen bonds : bond 0.03265 ( 956) hydrogen bonds : angle 4.04818 ( 2712) SS BOND : bond 0.00231 ( 10) SS BOND : angle 1.02553 ( 20) covalent geometry : bond 0.00225 (20746) covalent geometry : angle 0.51177 (28104) *********************** 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 295 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 2.069 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7364 (tt) cc_final: 0.7125 (pt) REVERT: A 170 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6831 (mp) REVERT: A 202 PHE cc_start: 0.7496 (p90) cc_final: 0.7214 (p90) REVERT: A 293 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.6878 (p90) REVERT: A 570 MET cc_start: 0.6422 (tpt) cc_final: 0.6101 (tpt) REVERT: A 582 TYR cc_start: 0.7281 (m-80) cc_final: 0.6939 (m-80) REVERT: A 1164 LYS cc_start: 0.5471 (mptt) cc_final: 0.4773 (mmtt) REVERT: A 1344 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8961 (mp) REVERT: D 77 GLN cc_start: 0.8562 (tp40) cc_final: 0.8179 (mp10) REVERT: D 80 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7810 (mt-10) REVERT: D 268 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9011 (m) REVERT: D 506 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9016 (mt) REVERT: D 879 ASP cc_start: 0.7893 (t70) cc_final: 0.7666 (t0) REVERT: C 196 MET cc_start: 0.6213 (mmp) cc_final: 0.5925 (tpp) REVERT: C 207 ARG cc_start: 0.6617 (tpp80) cc_final: 0.6391 (ttt180) outliers start: 39 outliers final: 21 residues processed: 281 average time/residue: 0.2788 time to fit residues: 127.6610 Evaluate side-chains 266 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 427 GLU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1121 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 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 972 GLN Chi-restraints excluded: chain D residue 1016 ILE 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 184 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 235 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 A1017 ASN ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132790 restraints weight = 25500.582| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.67 r_work: 0.3052 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20770 Z= 0.191 Angle : 0.598 11.127 28166 Z= 0.294 Chirality : 0.044 0.272 3201 Planarity : 0.004 0.049 3555 Dihedral : 7.094 81.288 3051 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.04 % Allowed : 14.48 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2472 helix: 1.19 (0.15), residues: 1215 sheet: -0.50 (0.32), residues: 275 loop : -1.25 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1103 HIS 0.004 0.001 HIS A 544 PHE 0.017 0.002 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.002 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 6) link_NAG-ASN : angle 4.05885 ( 18) link_BETA1-4 : bond 0.00713 ( 8) link_BETA1-4 : angle 2.65485 ( 24) hydrogen bonds : bond 0.03910 ( 956) hydrogen bonds : angle 4.20912 ( 2712) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.62581 ( 20) covalent geometry : bond 0.00467 (20746) covalent geometry : angle 0.58314 (28104) *********************** 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 285 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 2.310 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7402 (tt) cc_final: 0.7184 (pt) REVERT: A 170 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6688 (mp) REVERT: A 202 PHE cc_start: 0.7582 (p90) cc_final: 0.7250 (p90) REVERT: A 293 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.6940 (p90) REVERT: A 582 TYR cc_start: 0.7124 (m-80) cc_final: 0.6763 (m-80) REVERT: A 1150 PHE cc_start: 0.8419 (t80) cc_final: 0.8166 (t80) REVERT: A 1164 LYS cc_start: 0.5534 (mptt) cc_final: 0.4784 (mmtt) REVERT: A 1344 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9025 (mp) REVERT: D 77 GLN cc_start: 0.8601 (tp40) cc_final: 0.8209 (mp10) REVERT: D 268 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9022 (m) REVERT: D 506 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9038 (mt) REVERT: D 1009 MET cc_start: 0.8567 (tpt) cc_final: 0.8321 (tpt) outliers start: 45 outliers final: 32 residues processed: 266 average time/residue: 0.2977 time to fit residues: 129.9744 Evaluate side-chains 270 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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 621 VAL 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 965 VAL 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 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 625 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 798 VAL 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 C residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 158 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 225 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** C 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.175311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134411 restraints weight = 25946.869| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.83 r_work: 0.3059 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20770 Z= 0.145 Angle : 0.569 11.233 28166 Z= 0.279 Chirality : 0.043 0.282 3201 Planarity : 0.004 0.048 3555 Dihedral : 6.872 73.665 3051 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.99 % Allowed : 14.89 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2472 helix: 1.22 (0.15), residues: 1218 sheet: -0.55 (0.32), residues: 275 loop : -1.27 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1103 HIS 0.003 0.001 HIS A 544 PHE 0.018 0.001 PHE A1147 TYR 0.017 0.001 TYR D 719 ARG 0.002 0.000 ARG A1472 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 6) link_NAG-ASN : angle 4.02247 ( 18) link_BETA1-4 : bond 0.00693 ( 8) link_BETA1-4 : angle 2.71009 ( 24) hydrogen bonds : bond 0.03665 ( 956) hydrogen bonds : angle 4.15629 ( 2712) SS BOND : bond 0.00248 ( 10) SS BOND : angle 1.48570 ( 20) covalent geometry : bond 0.00348 (20746) covalent geometry : angle 0.55384 (28104) *********************** 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 278 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 2.247 Fit side-chains REVERT: A 130 ILE cc_start: 0.7385 (tt) cc_final: 0.7161 (pt) REVERT: A 170 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.6802 (mp) REVERT: A 202 PHE cc_start: 0.7668 (p90) cc_final: 0.7347 (p90) REVERT: A 293 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.6953 (p90) REVERT: A 582 TYR cc_start: 0.7167 (m-80) cc_final: 0.6822 (m-80) REVERT: A 616 SER cc_start: 0.8331 (t) cc_final: 0.8095 (m) REVERT: A 1150 PHE cc_start: 0.8379 (t80) cc_final: 0.8107 (t80) REVERT: A 1164 LYS cc_start: 0.5502 (mptt) cc_final: 0.4803 (mmtt) REVERT: A 1344 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9015 (mp) REVERT: D 77 GLN cc_start: 0.8613 (tp40) cc_final: 0.8207 (mp10) REVERT: D 80 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7852 (mt-10) REVERT: D 268 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9026 (m) REVERT: D 506 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9043 (mt) REVERT: D 1009 MET cc_start: 0.8565 (tpt) cc_final: 0.8327 (tpt) outliers start: 44 outliers final: 30 residues processed: 262 average time/residue: 0.2901 time to fit residues: 123.4691 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 965 VAL 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 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 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 707 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL 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 C residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 149 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 229 optimal weight: 30.0000 chunk 233 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A1114 ASN A1394 GLN ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136375 restraints weight = 25606.205| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.64 r_work: 0.3103 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20770 Z= 0.119 Angle : 0.555 11.060 28166 Z= 0.271 Chirality : 0.042 0.291 3201 Planarity : 0.003 0.047 3555 Dihedral : 6.562 63.961 3051 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.95 % Allowed : 15.16 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2472 helix: 1.33 (0.15), residues: 1217 sheet: -0.54 (0.32), residues: 275 loop : -1.22 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1474 HIS 0.002 0.000 HIS C 94 PHE 0.013 0.001 PHE A1147 TYR 0.017 0.001 TYR D 719 ARG 0.002 0.000 ARG A1472 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 6) link_NAG-ASN : angle 3.93232 ( 18) link_BETA1-4 : bond 0.00675 ( 8) link_BETA1-4 : angle 2.82202 ( 24) hydrogen bonds : bond 0.03410 ( 956) hydrogen bonds : angle 4.07586 ( 2712) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.36546 ( 20) covalent geometry : bond 0.00280 (20746) covalent geometry : angle 0.53884 (28104) *********************** 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 281 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 2.188 Fit side-chains REVERT: A 130 ILE cc_start: 0.7365 (tt) cc_final: 0.7137 (pt) REVERT: A 170 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6703 (mp) REVERT: A 202 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7390 (p90) REVERT: A 293 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.6896 (p90) REVERT: A 582 TYR cc_start: 0.7142 (m-80) cc_final: 0.6746 (m-80) REVERT: A 616 SER cc_start: 0.8340 (t) cc_final: 0.8102 (m) REVERT: A 1150 PHE cc_start: 0.8316 (t80) cc_final: 0.8029 (t80) REVERT: A 1164 LYS cc_start: 0.5488 (mptt) cc_final: 0.4807 (mmtt) REVERT: A 1344 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8961 (mp) REVERT: D 77 GLN cc_start: 0.8579 (tp40) cc_final: 0.8154 (mp10) REVERT: D 80 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7770 (mt-10) REVERT: D 268 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9029 (m) REVERT: D 506 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8968 (mt) REVERT: D 879 ASP cc_start: 0.8241 (t0) cc_final: 0.8026 (t0) REVERT: D 1009 MET cc_start: 0.8580 (tpt) cc_final: 0.8329 (tpt) outliers start: 43 outliers final: 29 residues processed: 263 average time/residue: 0.2963 time to fit residues: 126.8507 Evaluate side-chains 269 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 621 VAL 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 965 VAL Chi-restraints excluded: chain A residue 1146 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 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 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 707 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1016 ILE 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 202 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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 A1017 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.172307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133997 restraints weight = 26217.189| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.06 r_work: 0.2952 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20770 Z= 0.193 Angle : 0.615 11.155 28166 Z= 0.304 Chirality : 0.044 0.284 3201 Planarity : 0.004 0.048 3555 Dihedral : 6.600 59.553 3051 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.90 % Allowed : 15.79 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2472 helix: 1.19 (0.15), residues: 1216 sheet: -0.62 (0.31), residues: 275 loop : -1.31 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1474 HIS 0.004 0.001 HIS A 544 PHE 0.017 0.002 PHE A1447 TYR 0.014 0.001 TYR D1068 ARG 0.003 0.000 ARG A1173 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 6) link_NAG-ASN : angle 4.00065 ( 18) link_BETA1-4 : bond 0.00663 ( 8) link_BETA1-4 : angle 2.99198 ( 24) hydrogen bonds : bond 0.03966 ( 956) hydrogen bonds : angle 4.22712 ( 2712) SS BOND : bond 0.00316 ( 10) SS BOND : angle 1.84961 ( 20) covalent geometry : bond 0.00471 (20746) covalent geometry : angle 0.59935 (28104) ********************** 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 276 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 2.226 Fit side-chains REVERT: A 130 ILE cc_start: 0.7352 (tt) cc_final: 0.7110 (pt) REVERT: A 170 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6678 (mp) REVERT: A 202 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 293 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.7105 (p90) REVERT: A 582 TYR cc_start: 0.7158 (m-80) cc_final: 0.6730 (m-80) REVERT: A 1150 PHE cc_start: 0.8444 (t80) cc_final: 0.8195 (t80) REVERT: A 1164 LYS cc_start: 0.5571 (mptt) cc_final: 0.4815 (mmtt) REVERT: A 1344 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8999 (mp) REVERT: D 63 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7695 (ptpt) REVERT: D 77 GLN cc_start: 0.8709 (tp40) cc_final: 0.8267 (mp10) REVERT: D 80 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7945 (mt-10) REVERT: D 268 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9057 (m) REVERT: D 506 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9010 (mt) REVERT: D 859 LEU cc_start: 0.8808 (tt) cc_final: 0.8563 (tp) REVERT: D 1009 MET cc_start: 0.8578 (tpt) cc_final: 0.8328 (tpt) outliers start: 42 outliers final: 31 residues processed: 259 average time/residue: 0.2873 time to fit residues: 120.7466 Evaluate side-chains 268 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 427 GLU Chi-restraints excluded: chain A residue 621 VAL 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 965 VAL Chi-restraints excluded: chain A residue 1146 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 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 54 VAL Chi-restraints excluded: chain D residue 63 LYS 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 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1016 ILE 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 159 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135695 restraints weight = 25460.516| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.57 r_work: 0.3099 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1865 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= 0.107 Angle : 0.550 11.024 28166 Z= 0.269 Chirality : 0.041 0.282 3201 Planarity : 0.003 0.046 3555 Dihedral : 6.289 57.663 3051 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.54 % Allowed : 16.43 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2472 helix: 1.40 (0.15), residues: 1203 sheet: -0.55 (0.32), residues: 273 loop : -1.21 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1474 HIS 0.003 0.000 HIS C 94 PHE 0.013 0.001 PHE D 588 TYR 0.017 0.001 TYR D 719 ARG 0.005 0.000 ARG D 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 6) link_NAG-ASN : angle 3.90227 ( 18) link_BETA1-4 : bond 0.00704 ( 8) link_BETA1-4 : angle 2.86840 ( 24) hydrogen bonds : bond 0.03270 ( 956) hydrogen bonds : angle 4.04839 ( 2712) SS BOND : bond 0.00243 ( 10) SS BOND : angle 1.16304 ( 20) covalent geometry : bond 0.00245 (20746) covalent geometry : angle 0.53411 (28104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17473.19 seconds wall clock time: 311 minutes 25.89 seconds (18685.89 seconds total)