Starting phenix.real_space_refine on Thu Mar 5 09:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlq_33285/03_2026/7xlq_33285_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13081 2.51 5 N 3274 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10674 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1278} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 7637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7637 Classifications: {'peptide': 955} Link IDs: {'PTRANS': 42, 'TRANS': 912} Chain breaks: 3 Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1259 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 332 Unusual residues: {' CA': 1, '3PE': 1, 'R16': 7, 'Y01': 6} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {' CA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.44, per 1000 atoms: 0.22 Number of scatterers: 20132 At special positions: 0 Unit cell: (176.8, 114.4, 183.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3662 8.00 N 3274 7.00 C 13081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A1318 " - pdb=" SG CYS A1329 " distance=2.02 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1694 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 354 " - pdb=" SG CYS D1059 " 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=2.03 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 BETA1-3 " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN D 895 " " NAG D1201 " - " ASN D 604 " " NAG D1202 " - " ASN D 613 " " NAG D1203 " - " ASN D 675 " " NAG D1204 " - " ASN D 888 " " NAG D1205 " - " ASN D 184 " " NAG D1207 " - " ASN D 92 " " NAG D1208 " - " ASN D 324 " " NAG D1209 " - " ASN D 348 " " NAG E 1 " - " ASN D 468 " " NAG F 1 " - " ASN D 824 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 938.9 milliseconds 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 17 sheets defined 53.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.565A pdb=" N TYR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.698A pdb=" N ILE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 127 through 146 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 175 removed outlier: 4.049A pdb=" N MET A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.599A pdb=" N SER A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.660A pdb=" N GLN A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.554A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.805A pdb=" N PHE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.834A pdb=" N VAL A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.516A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 386 removed outlier: 3.950A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.675A pdb=" N LEU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.753A pdb=" N TRP A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.512A pdb=" N VAL A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 526 removed outlier: 3.539A pdb=" N HIS A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 560 removed outlier: 3.509A pdb=" N GLY A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.511A pdb=" N LEU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.694A pdb=" N LEU A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.528A pdb=" N VAL A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 removed outlier: 3.632A pdb=" N MET A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 removed outlier: 3.630A pdb=" N VAL A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 removed outlier: 3.794A pdb=" N ALA A 680 " --> pdb=" O MET A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.884A pdb=" N THR A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.550A pdb=" N ALA A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 removed outlier: 4.119A pdb=" N GLN A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 776 through 785 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 4.133A pdb=" N ASN A1151 " --> pdb=" O HIS A1147 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1147 through 1152' Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.640A pdb=" N CYS A1158 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1172 removed outlier: 3.723A pdb=" N ALA A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1207 removed outlier: 3.600A pdb=" N TYR A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1243 removed outlier: 3.878A pdb=" N LEU A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.819A pdb=" N ILE A1254 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 Proline residue: A1265 - end of helix Processing helix chain 'A' and resid 1267 through 1272 removed outlier: 3.848A pdb=" N ARG A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1287 removed outlier: 3.593A pdb=" N CYS A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing helix chain 'A' and resid 1307 through 1312 Processing helix chain 'A' and resid 1357 through 1370 removed outlier: 3.598A pdb=" N LEU A1365 " --> pdb=" O ALA A1361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A1368 " --> pdb=" O THR A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 3.621A pdb=" N HIS A1380 " --> pdb=" O GLN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1400 removed outlier: 3.508A pdb=" N SER A1400 " --> pdb=" O MET A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 3.567A pdb=" N PHE A1407 " --> pdb=" O TYR A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1425 removed outlier: 3.795A pdb=" N ASN A1416 " --> pdb=" O PHE A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 Processing helix chain 'A' and resid 1441 through 1447 Processing helix chain 'A' and resid 1467 through 1476 removed outlier: 5.568A pdb=" N HIS A1473 " --> pdb=" O TYR A1469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A1474 " --> pdb=" O ARG A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1505 through 1526 removed outlier: 3.906A pdb=" N VAL A1520 " --> pdb=" O ALA A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1533 Processing helix chain 'A' and resid 1533 through 1538 Processing helix chain 'A' and resid 1543 through 1560 removed outlier: 3.597A pdb=" N ILE A1548 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1550 " --> pdb=" O ASP A1546 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A1555 " --> pdb=" O ILE A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1574 removed outlier: 4.271A pdb=" N PHE A1574 " --> pdb=" O ASN A1571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1571 through 1574' Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 4.112A pdb=" N ARG A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1590 removed outlier: 3.689A pdb=" N ARG A1588 " --> pdb=" O LYS A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1603 Processing helix chain 'A' and resid 1609 through 1630 removed outlier: 3.734A pdb=" N ILE A1614 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A1615 " --> pdb=" O CYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1661 removed outlier: 3.514A pdb=" N LEU A1655 " --> pdb=" O GLY A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1671 Processing helix chain 'A' and resid 1698 through 1723 Processing helix chain 'A' and resid 1725 through 1730 Processing helix chain 'A' and resid 1737 through 1740 Processing helix chain 'A' and resid 1741 through 1753 removed outlier: 3.643A pdb=" N VAL A1745 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A1749 " --> pdb=" O VAL A1745 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1750 " --> pdb=" O ARG A1746 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR A1751 " --> pdb=" O VAL A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1771 removed outlier: 3.505A pdb=" N GLU A1766 " --> pdb=" O THR A1762 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1768 " --> pdb=" O MET A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1793 removed outlier: 4.061A pdb=" N ARG A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A1790 " --> pdb=" O ALA A1786 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A1791 " --> pdb=" O TYR A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1817 Processing helix chain 'A' and resid 1825 through 1843 removed outlier: 4.040A pdb=" N GLN A1829 " --> pdb=" O GLY A1825 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A1839 " --> pdb=" O LEU A1835 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A1841 " --> pdb=" O LYS A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1855 Processing helix chain 'A' and resid 1864 through 1871 Processing helix chain 'D' and resid 29 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 74 through 110 Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.543A pdb=" N ASP D 137 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 138' Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 4.000A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.506A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.739A 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 345 removed outlier: 3.660A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.846A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 431 removed outlier: 4.225A pdb=" N ASN D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 675 through 689 removed outlier: 3.553A pdb=" N ARG D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 719 removed outlier: 3.793A pdb=" N ILE D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.601A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 770 " --> pdb=" O ARG D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 Processing helix chain 'D' and resid 866 through 871 Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 890 removed outlier: 4.180A pdb=" N MET D 883 " --> pdb=" O ASP D 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.614A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 removed outlier: 3.705A pdb=" N LYS B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 393 through 412 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 253 Processing sheet with id=AA2, first strand: chain 'A' and resid 1316 through 1318 Processing sheet with id=AA3, first strand: chain 'A' and resid 1332 through 1335 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 142 through 144 removed outlier: 9.120A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.654A pdb=" N ARG D 157 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 215 through 217 removed outlier: 3.567A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 215 through 217 removed outlier: 3.567A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.179A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR D 409 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AB3, first strand: chain 'D' and resid 592 through 593 Processing sheet with id=AB4, first strand: chain 'D' and resid 729 through 736 removed outlier: 3.770A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 800 through 802 Processing sheet with id=AB6, first strand: chain 'D' and resid 859 through 862 removed outlier: 7.180A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 849 " --> pdb=" O VAL D1018 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D1018 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.681A pdb=" N PHE D 982 " --> pdb=" O ALA D 893 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.984A pdb=" N SER B 265 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP B 322 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR B 267 " --> pdb=" O ASP B 322 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 232 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 233 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 344 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 235 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 341 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 389 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR B 343 " --> pdb=" O LEU B 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 884 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3220 1.32 - 1.45: 5615 1.45 - 1.58: 11570 1.58 - 1.71: 2 1.71 - 1.84: 181 Bond restraints: 20588 Sorted by residual: bond pdb=" C TYR A 682 " pdb=" O TYR A 682 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.85e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C PRO D 529 " pdb=" O PRO D 529 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.79e+00 bond pdb=" N PRO D 529 " pdb=" CA PRO D 529 " ideal model delta sigma weight residual 1.469 1.429 0.040 1.28e-02 6.10e+03 9.57e+00 bond pdb=" N ILE A1620 " pdb=" CA ILE A1620 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.03e+00 ... (remaining 20583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 27603 3.23 - 6.45: 252 6.45 - 9.68: 17 9.68 - 12.91: 2 12.91 - 16.14: 2 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N SER A1479 " pdb=" CA SER A1479 " pdb=" C SER A1479 " ideal model delta sigma weight residual 114.09 101.02 13.07 1.55e+00 4.16e-01 7.11e+01 angle pdb=" CA CYS D 697 " pdb=" CB CYS D 697 " pdb=" SG CYS D 697 " ideal model delta sigma weight residual 114.40 130.54 -16.14 2.30e+00 1.89e-01 4.92e+01 angle pdb=" C GLY A 272 " pdb=" N CYS A 273 " pdb=" CA CYS A 273 " ideal model delta sigma weight residual 120.39 128.41 -8.02 1.39e+00 5.18e-01 3.33e+01 angle pdb=" CA CYS D 667 " pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " ideal model delta sigma weight residual 114.40 126.92 -12.52 2.30e+00 1.89e-01 2.96e+01 angle pdb=" N ILE A1294 " pdb=" CA ILE A1294 " pdb=" C ILE A1294 " ideal model delta sigma weight residual 111.90 107.78 4.12 8.10e-01 1.52e+00 2.58e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 11923 23.97 - 47.95: 759 47.95 - 71.92: 104 71.92 - 95.90: 31 95.90 - 119.87: 18 Dihedral angle restraints: 12835 sinusoidal: 5702 harmonic: 7133 Sorted by residual: dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual 93.00 -177.66 -89.34 1 1.00e+01 1.00e-02 9.49e+01 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 7.69 85.31 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA THR A 182 " pdb=" C THR A 182 " pdb=" N HIS A 183 " pdb=" CA HIS A 183 " ideal model delta harmonic sigma weight residual -180.00 -139.38 -40.62 0 5.00e+00 4.00e-02 6.60e+01 ... (remaining 12832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2712 0.068 - 0.137: 413 0.137 - 0.205: 27 0.205 - 0.274: 11 0.274 - 0.342: 3 Chirality restraints: 3166 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3163 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 204 " 0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 205 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 200 " -0.059 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO D 201 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 284 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 285 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.036 5.00e-02 4.00e+02 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 387 2.67 - 3.23: 19958 3.23 - 3.79: 29940 3.79 - 4.34: 43561 4.34 - 4.90: 69952 Nonbonded interactions: 163798 Sorted by model distance: nonbonded pdb=" O ASP D 596 " pdb=" OD1 ASP D 596 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASN D 481 " pdb=" O6 NAG E 1 " model vdw 2.177 3.040 nonbonded pdb=" O GLN D 528 " pdb=" NE2 GLN D 901 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR D 410 " pdb=" OE2 GLU D 412 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU A1556 " pdb=" NH1 ARG A1579 " model vdw 2.252 3.120 ... (remaining 163793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.006 0.076 20616 Z= 0.291 Angle : 0.875 16.137 27949 Z= 0.498 Chirality : 0.051 0.342 3166 Planarity : 0.005 0.096 3470 Dihedral : 16.121 119.873 8192 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer: Outliers : 0.33 % Allowed : 0.80 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.16), residues: 2414 helix: -2.51 (0.13), residues: 1187 sheet: -2.08 (0.32), residues: 244 loop : -1.91 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 240 TYR 0.030 0.002 TYR A 682 PHE 0.026 0.002 PHE D 711 TRP 0.028 0.002 TRP D 821 HIS 0.006 0.001 HIS D 885 Details of bonding type rmsd covalent geometry : bond 0.00616 (20588) covalent geometry : angle 0.85431 (27876) SS BOND : bond 0.00324 ( 11) SS BOND : angle 4.00869 ( 22) hydrogen bonds : bond 0.25915 ( 869) hydrogen bonds : angle 9.69172 ( 2481) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 4.26430 ( 3) link_BETA1-4 : bond 0.00563 ( 5) link_BETA1-4 : angle 1.66954 ( 15) link_NAG-ASN : bond 0.00457 ( 11) link_NAG-ASN : angle 4.29739 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 277 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: D 85 ASP cc_start: 0.7111 (m-30) cc_final: 0.6593 (m-30) REVERT: D 195 LYS cc_start: 0.7897 (tmmt) cc_final: 0.7576 (tmtt) REVERT: D 627 SER cc_start: 0.9000 (t) cc_final: 0.8387 (t) REVERT: D 683 PHE cc_start: 0.8190 (t80) cc_final: 0.7757 (t80) REVERT: B 229 MET cc_start: 0.4112 (mmt) cc_final: 0.3714 (mmt) outliers start: 7 outliers final: 4 residues processed: 283 average time/residue: 0.1439 time to fit residues: 64.5997 Evaluate side-chains 236 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1483 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 overall best weight: 0.1828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 541 ASN A1354 HIS A1416 ASN A1641 ASN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 391 GLN D 424 GLN D 482 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.216142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145195 restraints weight = 22548.840| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.37 r_work: 0.3465 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20616 Z= 0.133 Angle : 0.675 12.604 27949 Z= 0.348 Chirality : 0.044 0.211 3166 Planarity : 0.005 0.069 3470 Dihedral : 11.340 108.180 3517 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.80 % Allowed : 6.69 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.16), residues: 2414 helix: -1.36 (0.14), residues: 1239 sheet: -1.70 (0.31), residues: 255 loop : -1.67 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1389 TYR 0.024 0.001 TYR D 426 PHE 0.030 0.001 PHE D 733 TRP 0.019 0.001 TRP D 185 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00273 (20588) covalent geometry : angle 0.65688 (27876) SS BOND : bond 0.00231 ( 11) SS BOND : angle 2.74489 ( 22) hydrogen bonds : bond 0.05011 ( 869) hydrogen bonds : angle 5.44673 ( 2481) link_BETA1-3 : bond 0.00914 ( 1) link_BETA1-3 : angle 4.42948 ( 3) link_BETA1-4 : bond 0.00752 ( 5) link_BETA1-4 : angle 2.36413 ( 15) link_NAG-ASN : bond 0.00678 ( 11) link_NAG-ASN : angle 3.54560 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 284 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7742 (ttp) cc_final: 0.7273 (ttm) REVERT: A 527 MET cc_start: 0.4217 (ttt) cc_final: 0.3528 (mmt) REVERT: A 543 PHE cc_start: 0.7526 (t80) cc_final: 0.6793 (t80) REVERT: A 1433 MET cc_start: 0.4163 (ptp) cc_final: 0.3674 (ttt) REVERT: A 1434 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.5273 (ttm) REVERT: A 1728 TYR cc_start: 0.8653 (t80) cc_final: 0.8268 (t80) REVERT: A 1732 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: D 85 ASP cc_start: 0.7748 (m-30) cc_final: 0.7264 (m-30) REVERT: D 195 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7953 (tttt) REVERT: D 405 GLU cc_start: 0.7872 (tp30) cc_final: 0.7131 (tp30) REVERT: D 526 ASN cc_start: 0.8956 (t0) cc_final: 0.8756 (t0) REVERT: D 555 GLU cc_start: 0.8062 (pm20) cc_final: 0.7861 (pm20) REVERT: D 683 PHE cc_start: 0.8204 (t80) cc_final: 0.7690 (t80) REVERT: D 717 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7142 (mm-40) REVERT: D 1017 MET cc_start: 0.5622 (tpt) cc_final: 0.5245 (tpp) REVERT: D 1033 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7089 (tt0) outliers start: 17 outliers final: 8 residues processed: 296 average time/residue: 0.1383 time to fit residues: 65.4108 Evaluate side-chains 254 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1483 THR Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1033 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 179 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 221 optimal weight: 0.0970 chunk 227 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 HIS ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN ** D1004 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 = 0.4410 r_free = 0.4410 target = 0.213276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140604 restraints weight = 22448.343| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.32 r_work: 0.3397 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20616 Z= 0.159 Angle : 0.652 11.971 27949 Z= 0.329 Chirality : 0.045 0.273 3166 Planarity : 0.004 0.058 3470 Dihedral : 9.912 109.002 3515 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 1.64 % Allowed : 10.15 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2414 helix: -0.78 (0.14), residues: 1232 sheet: -1.48 (0.33), residues: 245 loop : -1.41 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1658 TYR 0.016 0.001 TYR D 426 PHE 0.014 0.001 PHE A1449 TRP 0.014 0.001 TRP D 185 HIS 0.005 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00367 (20588) covalent geometry : angle 0.63664 (27876) SS BOND : bond 0.00224 ( 11) SS BOND : angle 2.31424 ( 22) hydrogen bonds : bond 0.04321 ( 869) hydrogen bonds : angle 4.97238 ( 2481) link_BETA1-3 : bond 0.00862 ( 1) link_BETA1-3 : angle 4.42503 ( 3) link_BETA1-4 : bond 0.00616 ( 5) link_BETA1-4 : angle 2.27962 ( 15) link_NAG-ASN : bond 0.00419 ( 11) link_NAG-ASN : angle 3.23970 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 163 MET cc_start: 0.7576 (ttp) cc_final: 0.7272 (ttm) REVERT: A 530 MET cc_start: 0.8353 (ttp) cc_final: 0.8019 (ttp) REVERT: A 1433 MET cc_start: 0.4394 (ptp) cc_final: 0.3791 (ttt) REVERT: A 1434 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.5138 (ttm) REVERT: A 1732 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: D 195 LYS cc_start: 0.8245 (tmmt) cc_final: 0.7812 (pttt) REVERT: D 601 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: D 628 PHE cc_start: 0.8261 (m-80) cc_final: 0.7969 (m-10) REVERT: D 717 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7157 (mm-40) REVERT: D 1017 MET cc_start: 0.5292 (tpt) cc_final: 0.4954 (tpp) outliers start: 35 outliers final: 21 residues processed: 282 average time/residue: 0.1369 time to fit residues: 61.4421 Evaluate side-chains 272 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 3 optimal weight: 0.0010 chunk 183 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 HIS ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN ** D1004 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 = 0.4432 r_free = 0.4432 target = 0.215820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144844 restraints weight = 22649.146| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.35 r_work: 0.3458 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20616 Z= 0.123 Angle : 0.604 14.411 27949 Z= 0.305 Chirality : 0.043 0.204 3166 Planarity : 0.004 0.051 3470 Dihedral : 9.244 107.630 3513 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.97 % Allowed : 11.70 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2414 helix: -0.41 (0.15), residues: 1232 sheet: -1.33 (0.33), residues: 243 loop : -1.22 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1731 TYR 0.018 0.001 TYR D 426 PHE 0.013 0.001 PHE A1353 TRP 0.016 0.001 TRP D 185 HIS 0.018 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00271 (20588) covalent geometry : angle 0.58852 (27876) SS BOND : bond 0.00329 ( 11) SS BOND : angle 2.19047 ( 22) hydrogen bonds : bond 0.03688 ( 869) hydrogen bonds : angle 4.67758 ( 2481) link_BETA1-3 : bond 0.00775 ( 1) link_BETA1-3 : angle 4.23663 ( 3) link_BETA1-4 : bond 0.00582 ( 5) link_BETA1-4 : angle 2.22010 ( 15) link_NAG-ASN : bond 0.00630 ( 11) link_NAG-ASN : angle 3.12515 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.734 Fit side-chains REVERT: A 93 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 163 MET cc_start: 0.7492 (ttp) cc_final: 0.7261 (ttm) REVERT: A 332 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 472 MET cc_start: 0.5599 (ttt) cc_final: 0.5187 (ttp) REVERT: A 1433 MET cc_start: 0.4407 (ptp) cc_final: 0.3853 (ttt) REVERT: A 1464 ARG cc_start: 0.7100 (tmt170) cc_final: 0.6714 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: A 1732 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: D 85 ASP cc_start: 0.7483 (m-30) cc_final: 0.6949 (m-30) REVERT: D 195 LYS cc_start: 0.8187 (tmmt) cc_final: 0.7760 (pttt) REVERT: D 452 ASP cc_start: 0.7062 (t0) cc_final: 0.6818 (t0) REVERT: D 601 ASP cc_start: 0.7936 (t70) cc_final: 0.7384 (m-30) REVERT: D 627 SER cc_start: 0.8784 (t) cc_final: 0.8386 (t) REVERT: D 628 PHE cc_start: 0.8255 (m-80) cc_final: 0.7982 (m-10) REVERT: D 717 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7305 (mm-40) REVERT: D 736 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7954 (p) REVERT: D 883 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5929 (ptp) REVERT: D 1017 MET cc_start: 0.5152 (tpt) cc_final: 0.4934 (tpp) REVERT: B 247 MET cc_start: 0.5648 (tpt) cc_final: 0.4944 (mmm) outliers start: 42 outliers final: 19 residues processed: 290 average time/residue: 0.1410 time to fit residues: 64.9446 Evaluate side-chains 270 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 24 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN D 978 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.211531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139508 restraints weight = 22325.890| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.73 r_work: 0.3382 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20616 Z= 0.211 Angle : 0.658 12.232 27949 Z= 0.330 Chirality : 0.046 0.208 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.975 106.457 3513 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 2.39 % Allowed : 13.10 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2414 helix: -0.34 (0.15), residues: 1230 sheet: -1.31 (0.33), residues: 243 loop : -1.22 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 742 TYR 0.017 0.002 TYR D 426 PHE 0.023 0.002 PHE A1353 TRP 0.012 0.001 TRP A1374 HIS 0.011 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00507 (20588) covalent geometry : angle 0.64360 (27876) SS BOND : bond 0.00333 ( 11) SS BOND : angle 2.07712 ( 22) hydrogen bonds : bond 0.04001 ( 869) hydrogen bonds : angle 4.69384 ( 2481) link_BETA1-3 : bond 0.00828 ( 1) link_BETA1-3 : angle 3.81245 ( 3) link_BETA1-4 : bond 0.00581 ( 5) link_BETA1-4 : angle 2.00014 ( 15) link_NAG-ASN : bond 0.00411 ( 11) link_NAG-ASN : angle 3.22914 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 163 MET cc_start: 0.7726 (ttp) cc_final: 0.7357 (ttm) REVERT: A 291 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8856 (pm20) REVERT: A 332 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 1433 MET cc_start: 0.4631 (ptp) cc_final: 0.3629 (ttt) REVERT: A 1464 ARG cc_start: 0.7178 (tmt170) cc_final: 0.6699 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: A 1732 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: D 195 LYS cc_start: 0.8320 (tmmt) cc_final: 0.7929 (pttt) REVERT: D 452 ASP cc_start: 0.7331 (t0) cc_final: 0.6828 (t0) REVERT: D 601 ASP cc_start: 0.8002 (t70) cc_final: 0.7430 (m-30) REVERT: D 627 SER cc_start: 0.8740 (t) cc_final: 0.8506 (t) REVERT: D 628 PHE cc_start: 0.8365 (m-80) cc_final: 0.8097 (m-10) REVERT: D 717 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7442 (mm-40) REVERT: D 736 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8006 (p) REVERT: D 883 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6056 (ptp) REVERT: D 1017 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4940 (tpp) REVERT: B 247 MET cc_start: 0.5635 (tpt) cc_final: 0.4890 (mmm) outliers start: 51 outliers final: 33 residues processed: 288 average time/residue: 0.1404 time to fit residues: 65.3503 Evaluate side-chains 283 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 192 optimal weight: 9.9990 chunk 103 optimal weight: 0.0050 chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.214606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143695 restraints weight = 22402.984| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.62 r_work: 0.3448 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20616 Z= 0.121 Angle : 0.598 16.863 27949 Z= 0.301 Chirality : 0.043 0.197 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.685 105.846 3513 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.15 % Allowed : 14.13 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 2414 helix: -0.07 (0.15), residues: 1232 sheet: -1.18 (0.34), residues: 241 loop : -1.16 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 742 TYR 0.019 0.001 TYR D 426 PHE 0.016 0.001 PHE A1353 TRP 0.016 0.001 TRP D 185 HIS 0.009 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00272 (20588) covalent geometry : angle 0.58388 (27876) SS BOND : bond 0.00206 ( 11) SS BOND : angle 1.88430 ( 22) hydrogen bonds : bond 0.03458 ( 869) hydrogen bonds : angle 4.48442 ( 2481) link_BETA1-3 : bond 0.00826 ( 1) link_BETA1-3 : angle 3.58787 ( 3) link_BETA1-4 : bond 0.00477 ( 5) link_BETA1-4 : angle 1.71413 ( 15) link_NAG-ASN : bond 0.00564 ( 11) link_NAG-ASN : angle 3.09475 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7221 (t80) REVERT: A 163 MET cc_start: 0.7655 (ttp) cc_final: 0.7367 (ttm) REVERT: A 293 ASP cc_start: 0.8578 (m-30) cc_final: 0.8344 (m-30) REVERT: A 332 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 357 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 472 MET cc_start: 0.5566 (ttt) cc_final: 0.5158 (ttp) REVERT: A 1194 THR cc_start: 0.8179 (m) cc_final: 0.7899 (m) REVERT: A 1433 MET cc_start: 0.4510 (ptp) cc_final: 0.3511 (ttt) REVERT: A 1464 ARG cc_start: 0.7085 (tmt170) cc_final: 0.6713 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: A 1732 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: A 1795 MET cc_start: 0.6258 (mmm) cc_final: 0.4055 (ppp) REVERT: D 85 ASP cc_start: 0.7605 (m-30) cc_final: 0.7126 (m-30) REVERT: D 195 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7921 (pttt) REVERT: D 452 ASP cc_start: 0.7199 (t0) cc_final: 0.6840 (t0) REVERT: D 601 ASP cc_start: 0.7965 (t70) cc_final: 0.7519 (m-30) REVERT: D 627 SER cc_start: 0.8550 (t) cc_final: 0.8264 (t) REVERT: D 628 PHE cc_start: 0.8230 (m-80) cc_final: 0.7745 (m-10) REVERT: D 717 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7453 (mm-40) REVERT: D 736 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7928 (p) REVERT: D 883 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6062 (ptp) REVERT: D 1017 MET cc_start: 0.5119 (tpt) cc_final: 0.4895 (tpp) REVERT: B 247 MET cc_start: 0.5737 (tpt) cc_final: 0.5024 (mmm) outliers start: 46 outliers final: 36 residues processed: 290 average time/residue: 0.1417 time to fit residues: 65.6888 Evaluate side-chains 289 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 161 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 103 optimal weight: 0.0170 chunk 139 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.210912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137509 restraints weight = 22301.826| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.36 r_work: 0.3410 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20616 Z= 0.127 Angle : 0.591 14.879 27949 Z= 0.297 Chirality : 0.043 0.196 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.543 106.463 3513 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.62 % Allowed : 14.23 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2414 helix: 0.08 (0.15), residues: 1241 sheet: -1.10 (0.34), residues: 241 loop : -1.10 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 766 TYR 0.017 0.001 TYR D 426 PHE 0.018 0.001 PHE D 686 TRP 0.014 0.001 TRP D 185 HIS 0.009 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00291 (20588) covalent geometry : angle 0.57787 (27876) SS BOND : bond 0.00275 ( 11) SS BOND : angle 1.77813 ( 22) hydrogen bonds : bond 0.03390 ( 869) hydrogen bonds : angle 4.40218 ( 2481) link_BETA1-3 : bond 0.00837 ( 1) link_BETA1-3 : angle 3.43845 ( 3) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 1.64726 ( 15) link_NAG-ASN : bond 0.00474 ( 11) link_NAG-ASN : angle 3.07248 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7326 (t80) REVERT: A 163 MET cc_start: 0.7713 (ttp) cc_final: 0.7431 (ttm) REVERT: A 293 ASP cc_start: 0.8668 (m-30) cc_final: 0.8408 (m-30) REVERT: A 332 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 357 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8600 (tm-30) REVERT: A 472 MET cc_start: 0.5598 (ttt) cc_final: 0.5171 (ttp) REVERT: A 1156 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6203 (pt0) REVERT: A 1157 MET cc_start: 0.7387 (tmm) cc_final: 0.7117 (tpp) REVERT: A 1194 THR cc_start: 0.8200 (m) cc_final: 0.7896 (m) REVERT: A 1433 MET cc_start: 0.4551 (ptp) cc_final: 0.3662 (ttt) REVERT: A 1627 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: A 1732 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: A 1795 MET cc_start: 0.6167 (mmm) cc_final: 0.4009 (ppp) REVERT: D 85 ASP cc_start: 0.7656 (m-30) cc_final: 0.7174 (m-30) REVERT: D 195 LYS cc_start: 0.8256 (tmmt) cc_final: 0.7893 (pttt) REVERT: D 452 ASP cc_start: 0.7216 (t0) cc_final: 0.6884 (t0) REVERT: D 601 ASP cc_start: 0.8030 (t70) cc_final: 0.7592 (m-30) REVERT: D 627 SER cc_start: 0.8691 (t) cc_final: 0.8413 (t) REVERT: D 628 PHE cc_start: 0.8306 (m-80) cc_final: 0.7804 (m-10) REVERT: D 736 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7987 (p) REVERT: D 848 MET cc_start: 0.0997 (mmt) cc_final: 0.0570 (mmm) REVERT: D 883 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6113 (ptp) REVERT: D 1042 ASN cc_start: 0.8365 (t0) cc_final: 0.8060 (t0) REVERT: B 247 MET cc_start: 0.5728 (tpt) cc_final: 0.4950 (mmm) outliers start: 56 outliers final: 35 residues processed: 296 average time/residue: 0.1400 time to fit residues: 65.9419 Evaluate side-chains 291 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.210917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138829 restraints weight = 22348.315| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.38 r_work: 0.3396 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20616 Z= 0.132 Angle : 0.597 13.580 27949 Z= 0.300 Chirality : 0.043 0.193 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.459 106.108 3513 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.34 % Allowed : 14.55 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2414 helix: 0.16 (0.15), residues: 1241 sheet: -1.10 (0.34), residues: 243 loop : -1.11 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1464 TYR 0.017 0.001 TYR D 426 PHE 0.018 0.001 PHE D 686 TRP 0.014 0.001 TRP D 185 HIS 0.011 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00307 (20588) covalent geometry : angle 0.58354 (27876) SS BOND : bond 0.00242 ( 11) SS BOND : angle 2.08753 ( 22) hydrogen bonds : bond 0.03362 ( 869) hydrogen bonds : angle 4.36482 ( 2481) link_BETA1-3 : bond 0.00881 ( 1) link_BETA1-3 : angle 3.30122 ( 3) link_BETA1-4 : bond 0.00535 ( 5) link_BETA1-4 : angle 1.58556 ( 15) link_NAG-ASN : bond 0.00519 ( 11) link_NAG-ASN : angle 3.04707 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7139 (t80) REVERT: A 163 MET cc_start: 0.7512 (ttp) cc_final: 0.7240 (ttm) REVERT: A 293 ASP cc_start: 0.8556 (m-30) cc_final: 0.8351 (m-30) REVERT: A 332 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 357 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8448 (tm-30) REVERT: A 472 MET cc_start: 0.5482 (ttt) cc_final: 0.5087 (ttp) REVERT: A 1156 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6183 (pt0) REVERT: A 1157 MET cc_start: 0.7215 (tmm) cc_final: 0.6969 (tpp) REVERT: A 1194 THR cc_start: 0.8164 (m) cc_final: 0.7862 (m) REVERT: A 1433 MET cc_start: 0.4449 (ptp) cc_final: 0.3620 (ttt) REVERT: A 1464 ARG cc_start: 0.6542 (tpt90) cc_final: 0.6129 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: A 1795 MET cc_start: 0.6289 (mmm) cc_final: 0.4183 (ppp) REVERT: D 85 ASP cc_start: 0.7469 (m-30) cc_final: 0.6931 (m-30) REVERT: D 195 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7831 (pttt) REVERT: D 452 ASP cc_start: 0.7018 (t0) cc_final: 0.6733 (t0) REVERT: D 601 ASP cc_start: 0.7840 (t70) cc_final: 0.7453 (m-30) REVERT: D 627 SER cc_start: 0.8671 (t) cc_final: 0.8376 (t) REVERT: D 628 PHE cc_start: 0.8222 (m-80) cc_final: 0.7726 (m-10) REVERT: D 736 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7882 (p) REVERT: D 848 MET cc_start: 0.0900 (mmt) cc_final: 0.0490 (mmm) REVERT: D 883 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6151 (ptp) REVERT: D 1042 ASN cc_start: 0.8299 (t0) cc_final: 0.8001 (t0) REVERT: B 247 MET cc_start: 0.5584 (tpt) cc_final: 0.3638 (mtp) outliers start: 50 outliers final: 39 residues processed: 291 average time/residue: 0.1296 time to fit residues: 60.6975 Evaluate side-chains 291 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 90 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.211187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136926 restraints weight = 22185.301| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.20 r_work: 0.3447 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20616 Z= 0.130 Angle : 0.592 12.411 27949 Z= 0.298 Chirality : 0.043 0.191 3166 Planarity : 0.004 0.049 3470 Dihedral : 8.393 105.765 3513 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.29 % Allowed : 14.88 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2414 helix: 0.24 (0.15), residues: 1243 sheet: -1.07 (0.35), residues: 243 loop : -1.07 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 766 TYR 0.017 0.001 TYR D 426 PHE 0.019 0.001 PHE D 686 TRP 0.015 0.001 TRP D 185 HIS 0.005 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00300 (20588) covalent geometry : angle 0.57900 (27876) SS BOND : bond 0.00218 ( 11) SS BOND : angle 1.94107 ( 22) hydrogen bonds : bond 0.03332 ( 869) hydrogen bonds : angle 4.32643 ( 2481) link_BETA1-3 : bond 0.00830 ( 1) link_BETA1-3 : angle 3.23724 ( 3) link_BETA1-4 : bond 0.00557 ( 5) link_BETA1-4 : angle 1.53970 ( 15) link_NAG-ASN : bond 0.00547 ( 11) link_NAG-ASN : angle 3.00434 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7115 (t80) REVERT: A 163 MET cc_start: 0.7707 (ttp) cc_final: 0.7410 (ttm) REVERT: A 293 ASP cc_start: 0.8688 (m-30) cc_final: 0.8436 (m-30) REVERT: A 332 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 357 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 472 MET cc_start: 0.5554 (ttt) cc_final: 0.5140 (ttp) REVERT: A 1156 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6214 (pt0) REVERT: A 1157 MET cc_start: 0.7336 (tmm) cc_final: 0.7080 (tpp) REVERT: A 1194 THR cc_start: 0.8193 (m) cc_final: 0.7897 (m) REVERT: A 1433 MET cc_start: 0.4454 (ptp) cc_final: 0.3631 (ttt) REVERT: A 1464 ARG cc_start: 0.6504 (tpt90) cc_final: 0.6082 (tpt-90) REVERT: A 1522 SER cc_start: 0.8846 (t) cc_final: 0.8358 (m) REVERT: A 1627 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: A 1795 MET cc_start: 0.6275 (mmm) cc_final: 0.4194 (ppp) REVERT: D 85 ASP cc_start: 0.7619 (m-30) cc_final: 0.7100 (m-30) REVERT: D 195 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7907 (pttt) REVERT: D 371 GLU cc_start: 0.8258 (tp30) cc_final: 0.7869 (tp30) REVERT: D 452 ASP cc_start: 0.7122 (t0) cc_final: 0.6830 (t0) REVERT: D 601 ASP cc_start: 0.7854 (t70) cc_final: 0.7408 (m-30) REVERT: D 627 SER cc_start: 0.8619 (t) cc_final: 0.8342 (t) REVERT: D 628 PHE cc_start: 0.8285 (m-80) cc_final: 0.7771 (m-10) REVERT: D 736 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7912 (p) REVERT: D 848 MET cc_start: 0.0963 (mmt) cc_final: 0.0549 (mmm) REVERT: D 883 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6225 (ptp) REVERT: D 1042 ASN cc_start: 0.8349 (t0) cc_final: 0.8040 (t0) REVERT: B 247 MET cc_start: 0.5612 (tpt) cc_final: 0.3672 (mtp) outliers start: 49 outliers final: 39 residues processed: 286 average time/residue: 0.1328 time to fit residues: 61.3840 Evaluate side-chains 289 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 768 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 198 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 228 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 179 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.211907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138988 restraints weight = 22400.174| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.31 r_work: 0.3406 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20616 Z= 0.119 Angle : 0.589 11.538 27949 Z= 0.296 Chirality : 0.042 0.186 3166 Planarity : 0.004 0.049 3470 Dihedral : 8.342 105.890 3513 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.06 % Allowed : 15.40 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2414 helix: 0.35 (0.15), residues: 1243 sheet: -1.00 (0.35), residues: 242 loop : -1.07 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 766 TYR 0.017 0.001 TYR D 744 PHE 0.021 0.001 PHE D 686 TRP 0.016 0.001 TRP D 185 HIS 0.005 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00272 (20588) covalent geometry : angle 0.57273 (27876) SS BOND : bond 0.00201 ( 11) SS BOND : angle 2.94912 ( 22) hydrogen bonds : bond 0.03228 ( 869) hydrogen bonds : angle 4.27818 ( 2481) link_BETA1-3 : bond 0.00858 ( 1) link_BETA1-3 : angle 3.15676 ( 3) link_BETA1-4 : bond 0.00602 ( 5) link_BETA1-4 : angle 1.50768 ( 15) link_NAG-ASN : bond 0.00677 ( 11) link_NAG-ASN : angle 2.96143 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.6921 (t80) REVERT: A 163 MET cc_start: 0.7529 (ttp) cc_final: 0.7259 (ttm) REVERT: A 293 ASP cc_start: 0.8577 (m-30) cc_final: 0.8373 (m-30) REVERT: A 332 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 357 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 472 MET cc_start: 0.5437 (ttt) cc_final: 0.5041 (ttp) REVERT: A 1156 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6247 (pt0) REVERT: A 1157 MET cc_start: 0.7189 (tmm) cc_final: 0.6980 (tpp) REVERT: A 1194 THR cc_start: 0.8142 (m) cc_final: 0.7842 (m) REVERT: A 1433 MET cc_start: 0.4502 (ptp) cc_final: 0.3735 (ttt) REVERT: A 1464 ARG cc_start: 0.6541 (tpt90) cc_final: 0.6050 (tpt-90) REVERT: A 1522 SER cc_start: 0.8771 (t) cc_final: 0.8291 (m) REVERT: A 1627 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: A 1795 MET cc_start: 0.6238 (mmm) cc_final: 0.4135 (ppp) REVERT: D 85 ASP cc_start: 0.7450 (m-30) cc_final: 0.6901 (m-30) REVERT: D 195 LYS cc_start: 0.8178 (tmmt) cc_final: 0.7819 (pttt) REVERT: D 371 GLU cc_start: 0.8152 (tp30) cc_final: 0.7596 (mp0) REVERT: D 452 ASP cc_start: 0.6895 (t0) cc_final: 0.6695 (t0) REVERT: D 601 ASP cc_start: 0.7879 (t70) cc_final: 0.7428 (m-30) REVERT: D 627 SER cc_start: 0.8628 (t) cc_final: 0.8340 (t) REVERT: D 628 PHE cc_start: 0.8200 (m-80) cc_final: 0.7710 (m-10) REVERT: D 736 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7872 (p) REVERT: D 848 MET cc_start: 0.0961 (mmt) cc_final: 0.0552 (mmm) REVERT: D 877 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 883 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6179 (ptp) REVERT: D 1042 ASN cc_start: 0.8277 (t0) cc_final: 0.7980 (t0) REVERT: B 247 MET cc_start: 0.5551 (tpt) cc_final: 0.3651 (mtp) outliers start: 44 outliers final: 38 residues processed: 280 average time/residue: 0.1404 time to fit residues: 63.2572 Evaluate side-chains 287 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1627 GLN Chi-restraints excluded: chain A residue 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 768 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 883 MET Chi-restraints excluded: chain D residue 904 CYS Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1033 GLN Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 88 optimal weight: 20.0000 chunk 61 optimal weight: 0.0270 chunk 198 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A1354 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 509 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.207314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132931 restraints weight = 22264.212| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.29 r_work: 0.3345 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20616 Z= 0.242 Angle : 0.671 10.976 27949 Z= 0.337 Chirality : 0.046 0.202 3166 Planarity : 0.004 0.049 3470 Dihedral : 8.560 105.739 3513 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.06 % Allowed : 15.44 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2414 helix: 0.08 (0.15), residues: 1247 sheet: -1.08 (0.34), residues: 252 loop : -1.21 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 766 TYR 0.018 0.002 TYR D 744 PHE 0.028 0.002 PHE A1353 TRP 0.014 0.002 TRP A 282 HIS 0.020 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00587 (20588) covalent geometry : angle 0.65649 (27876) SS BOND : bond 0.00349 ( 11) SS BOND : angle 3.03127 ( 22) hydrogen bonds : bond 0.03900 ( 869) hydrogen bonds : angle 4.49810 ( 2481) link_BETA1-3 : bond 0.00913 ( 1) link_BETA1-3 : angle 2.98898 ( 3) link_BETA1-4 : bond 0.00546 ( 5) link_BETA1-4 : angle 1.60859 ( 15) link_NAG-ASN : bond 0.00502 ( 11) link_NAG-ASN : angle 3.09582 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6880.12 seconds wall clock time: 117 minutes 54.96 seconds (7074.96 seconds total)