Starting phenix.real_space_refine on Wed Jun 18 08:26:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xlq_33285/06_2025/7xlq_33285_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlq_33285/06_2025/7xlq_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_33285/06_2025/7xlq_33285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlq_33285/06_2025/7xlq_33285.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlq_33285/06_2025/7xlq_33285_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlq_33285/06_2025/7xlq_33285_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.103 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 2, 'ASP:plan': 1} 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: 12.15, per 1000 atoms: 0.60 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: 5.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.45 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: 7.76 Time building geometry restraints manager: 6.30 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 47.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- 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 : 12.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP D 821 HIS 0.006 0.001 HIS D 885 PHE 0.026 0.002 PHE D 711 TYR 0.030 0.002 TYR A 682 ARG 0.007 0.001 ARG D 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 11) link_NAG-ASN : angle 4.29739 ( 33) link_BETA1-4 : bond 0.00563 ( 5) link_BETA1-4 : angle 1.66954 ( 15) hydrogen bonds : bond 0.25915 ( 869) hydrogen bonds : angle 9.69172 ( 2481) SS BOND : bond 0.00324 ( 11) SS BOND : angle 4.00869 ( 22) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 4.26430 ( 3) covalent geometry : bond 0.00616 (20588) covalent geometry : angle 0.85431 (27876) *********************** 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 : 2.397 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: 0.3417 time to fit residues: 152.6641 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 : 2.420 ------------------------------------------------------------------------------- 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 204 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 141 optimal weight: 0.0670 chunk 219 optimal weight: 10.0000 overall best weight: 0.7324 ------------------------------------------------------------------------------- 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 A1641 ASN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.213511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139988 restraints weight = 22265.706| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.26 r_work: 0.3457 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20616 Z= 0.153 Angle : 0.693 12.817 27949 Z= 0.356 Chirality : 0.045 0.218 3166 Planarity : 0.005 0.070 3470 Dihedral : 11.273 107.229 3517 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 0.94 % Allowed : 7.49 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.16), residues: 2414 helix: -1.41 (0.14), residues: 1239 sheet: -1.68 (0.32), residues: 243 loop : -1.69 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 185 HIS 0.005 0.001 HIS A1639 PHE 0.031 0.002 PHE D 733 TYR 0.024 0.001 TYR D 426 ARG 0.005 0.001 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 11) link_NAG-ASN : angle 3.58915 ( 33) link_BETA1-4 : bond 0.00646 ( 5) link_BETA1-4 : angle 2.46449 ( 15) hydrogen bonds : bond 0.04846 ( 869) hydrogen bonds : angle 5.43800 ( 2481) SS BOND : bond 0.00282 ( 11) SS BOND : angle 2.73971 ( 22) link_BETA1-3 : bond 0.00818 ( 1) link_BETA1-3 : angle 4.60775 ( 3) covalent geometry : bond 0.00338 (20588) covalent geometry : angle 0.67463 (27876) *********************** 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 299 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7729 (ttp) cc_final: 0.7278 (ttm) REVERT: A 527 MET cc_start: 0.4404 (ttt) cc_final: 0.3569 (mmt) REVERT: A 543 PHE cc_start: 0.7568 (t80) cc_final: 0.6845 (t80) REVERT: A 1433 MET cc_start: 0.4202 (ptp) cc_final: 0.3682 (ttt) REVERT: A 1434 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.5274 (ttm) REVERT: A 1732 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: D 85 ASP cc_start: 0.7764 (m-30) cc_final: 0.7298 (m-30) REVERT: D 195 LYS cc_start: 0.8394 (tmmt) cc_final: 0.7775 (pttt) REVERT: D 452 ASP cc_start: 0.7640 (t0) cc_final: 0.7291 (t0) REVERT: D 555 GLU cc_start: 0.8071 (pm20) cc_final: 0.7806 (pm20) REVERT: D 678 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 683 PHE cc_start: 0.8201 (t80) cc_final: 0.7705 (t80) REVERT: D 717 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7199 (mm-40) REVERT: D 1017 MET cc_start: 0.5442 (tpt) cc_final: 0.5031 (tpp) outliers start: 20 outliers final: 12 residues processed: 290 average time/residue: 0.3119 time to fit residues: 143.7172 Evaluate side-chains 259 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 713 THR 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 Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 71 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 HIS A1416 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.213232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140771 restraints weight = 22286.185| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.21 r_work: 0.3421 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20616 Z= 0.153 Angle : 0.647 11.910 27949 Z= 0.327 Chirality : 0.045 0.268 3166 Planarity : 0.004 0.057 3470 Dihedral : 9.811 109.089 3514 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.33 % Rotamer: Outliers : 1.73 % Allowed : 10.81 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2414 helix: -0.78 (0.14), residues: 1235 sheet: -1.54 (0.31), residues: 259 loop : -1.41 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.004 0.001 HIS A1336 PHE 0.015 0.001 PHE A1199 TYR 0.019 0.001 TYR D 426 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 11) link_NAG-ASN : angle 3.22668 ( 33) link_BETA1-4 : bond 0.00626 ( 5) link_BETA1-4 : angle 2.29629 ( 15) hydrogen bonds : bond 0.04247 ( 869) hydrogen bonds : angle 4.94300 ( 2481) SS BOND : bond 0.00221 ( 11) SS BOND : angle 2.25897 ( 22) link_BETA1-3 : bond 0.00926 ( 1) link_BETA1-3 : angle 4.38527 ( 3) covalent geometry : bond 0.00354 (20588) covalent geometry : angle 0.63101 (27876) *********************** 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 306 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 2.248 Fit side-chains revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7344 (t80) REVERT: A 163 MET cc_start: 0.7472 (ttp) cc_final: 0.7229 (ttm) REVERT: A 294 ASN cc_start: 0.8350 (m-40) cc_final: 0.8124 (m-40) REVERT: A 530 MET cc_start: 0.8343 (ttp) cc_final: 0.8053 (ttp) REVERT: A 1433 MET cc_start: 0.4491 (ptp) cc_final: 0.3687 (ttt) REVERT: A 1732 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 1771 MET cc_start: 0.4392 (ptp) cc_final: 0.4019 (ppp) REVERT: D 195 LYS cc_start: 0.8203 (tmmt) cc_final: 0.7778 (pttt) REVERT: D 601 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: D 678 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 717 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7239 (mm-40) REVERT: D 775 PHE cc_start: 0.8610 (m-80) cc_final: 0.8350 (m-80) REVERT: D 1017 MET cc_start: 0.5225 (tpt) cc_final: 0.4867 (tpp) REVERT: B 247 MET cc_start: 0.5591 (tpt) cc_final: 0.4890 (mmm) outliers start: 37 outliers final: 19 residues processed: 284 average time/residue: 0.3121 time to fit residues: 139.2710 Evaluate side-chains 267 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain A residue 373 GLN 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 1732 ASP Chi-restraints excluded: chain A residue 1739 HIS 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 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 108 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN 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 D 978 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.211945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138392 restraints weight = 22393.518| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.27 r_work: 0.3382 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20616 Z= 0.185 Angle : 0.644 13.699 27949 Z= 0.324 Chirality : 0.045 0.211 3166 Planarity : 0.004 0.052 3470 Dihedral : 9.298 107.489 3513 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.53 % Allowed : 12.35 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2414 helix: -0.57 (0.15), residues: 1229 sheet: -1.44 (0.31), residues: 261 loop : -1.37 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.015 0.001 HIS A1354 PHE 0.015 0.001 PHE A 553 TYR 0.018 0.001 TYR D 426 ARG 0.007 0.000 ARG A1350 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 11) link_NAG-ASN : angle 3.21942 ( 33) link_BETA1-4 : bond 0.00559 ( 5) link_BETA1-4 : angle 2.26680 ( 15) hydrogen bonds : bond 0.04035 ( 869) hydrogen bonds : angle 4.79348 ( 2481) SS BOND : bond 0.00347 ( 11) SS BOND : angle 2.26586 ( 22) link_BETA1-3 : bond 0.00812 ( 1) link_BETA1-3 : angle 4.23124 ( 3) covalent geometry : bond 0.00442 (20588) covalent geometry : angle 0.62783 (27876) *********************** 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: 54 poor density : 253 time to evaluate : 2.410 Fit side-chains REVERT: A 93 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 163 MET cc_start: 0.7544 (ttp) cc_final: 0.7263 (ttm) REVERT: A 332 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 518 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7342 (tt) REVERT: A 1433 MET cc_start: 0.4343 (ptp) cc_final: 0.3696 (ttt) REVERT: A 1464 ARG cc_start: 0.7035 (tmt170) cc_final: 0.6638 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: A 1732 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: A 1771 MET cc_start: 0.4405 (ptp) cc_final: 0.4130 (ppp) REVERT: A 1795 MET cc_start: 0.4525 (mtt) cc_final: 0.3428 (ppp) REVERT: D 195 LYS cc_start: 0.8248 (tmmt) cc_final: 0.7838 (pttt) REVERT: D 452 ASP cc_start: 0.7463 (t0) cc_final: 0.7164 (t0) REVERT: D 601 ASP cc_start: 0.7909 (t70) cc_final: 0.7430 (m-30) REVERT: D 678 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 717 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7315 (mm-40) REVERT: D 736 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7954 (p) REVERT: D 775 PHE cc_start: 0.8549 (m-80) cc_final: 0.8251 (m-80) REVERT: D 883 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5916 (ptp) REVERT: D 1017 MET cc_start: 0.5230 (tpt) cc_final: 0.4976 (tpp) REVERT: B 247 MET cc_start: 0.5623 (tpt) cc_final: 0.4901 (mmm) outliers start: 54 outliers final: 32 residues processed: 283 average time/residue: 0.3098 time to fit residues: 140.6061 Evaluate side-chains 282 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 281 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 ILE 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 1284 THR Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1487 MET 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 123 VAL Chi-restraints excluded: chain D residue 287 ASP 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 461 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 13 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 196 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.213025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139640 restraints weight = 22377.448| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.33 r_work: 0.3421 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20616 Z= 0.149 Angle : 0.616 12.701 27949 Z= 0.311 Chirality : 0.044 0.204 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.876 106.599 3513 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 2.34 % Allowed : 13.43 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2414 helix: -0.35 (0.15), residues: 1232 sheet: -1.41 (0.31), residues: 261 loop : -1.29 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.010 0.001 HIS A1354 PHE 0.021 0.001 PHE A 297 TYR 0.019 0.001 TYR D 426 ARG 0.006 0.000 ARG D 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 11) link_NAG-ASN : angle 3.13290 ( 33) link_BETA1-4 : bond 0.00569 ( 5) link_BETA1-4 : angle 1.96490 ( 15) hydrogen bonds : bond 0.03730 ( 869) hydrogen bonds : angle 4.61989 ( 2481) SS BOND : bond 0.00341 ( 11) SS BOND : angle 2.02302 ( 22) link_BETA1-3 : bond 0.00816 ( 1) link_BETA1-3 : angle 3.85683 ( 3) covalent geometry : bond 0.00348 (20588) covalent geometry : angle 0.60204 (27876) *********************** 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 313 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 163 MET cc_start: 0.7789 (ttp) cc_final: 0.7483 (ttm) REVERT: A 332 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 357 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 1433 MET cc_start: 0.4572 (ptp) cc_final: 0.3615 (ttt) REVERT: A 1464 ARG cc_start: 0.7027 (tmt170) cc_final: 0.6643 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: A 1732 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: A 1771 MET cc_start: 0.4387 (ptp) cc_final: 0.4111 (ppp) REVERT: D 85 ASP cc_start: 0.7747 (m-30) cc_final: 0.7278 (m-30) REVERT: D 195 LYS cc_start: 0.8339 (tmmt) cc_final: 0.7959 (pttt) REVERT: D 452 ASP cc_start: 0.7584 (t0) cc_final: 0.7280 (t0) REVERT: D 601 ASP cc_start: 0.8122 (t70) cc_final: 0.7521 (m-30) REVERT: D 678 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 736 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 775 PHE cc_start: 0.8609 (m-80) cc_final: 0.8326 (m-80) REVERT: D 883 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6048 (ptp) REVERT: D 1017 MET cc_start: 0.5216 (OUTLIER) cc_final: 0.4957 (tpp) REVERT: B 247 MET cc_start: 0.5740 (tpt) cc_final: 0.5001 (mmm) outliers start: 50 outliers final: 34 residues processed: 290 average time/residue: 0.2997 time to fit residues: 139.0270 Evaluate side-chains 287 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 MET 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 1367 THR Chi-restraints excluded: chain A residue 1487 MET 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 122 VAL 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 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 126 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 183 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 188 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 537 HIS 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 870 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.215522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142571 restraints weight = 22414.158| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.09 r_work: 0.3491 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20616 Z= 0.117 Angle : 0.592 16.994 27949 Z= 0.297 Chirality : 0.042 0.197 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.619 105.733 3513 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.53 % Allowed : 14.27 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2414 helix: -0.09 (0.15), residues: 1232 sheet: -1.25 (0.32), residues: 257 loop : -1.25 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.007 0.001 HIS A1354 PHE 0.019 0.001 PHE A 553 TYR 0.018 0.001 TYR D 426 ARG 0.005 0.000 ARG D 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 11) link_NAG-ASN : angle 3.01571 ( 33) link_BETA1-4 : bond 0.00533 ( 5) link_BETA1-4 : angle 1.71064 ( 15) hydrogen bonds : bond 0.03435 ( 869) hydrogen bonds : angle 4.46312 ( 2481) SS BOND : bond 0.00820 ( 11) SS BOND : angle 1.81283 ( 22) link_BETA1-3 : bond 0.00907 ( 1) link_BETA1-3 : angle 3.58280 ( 3) covalent geometry : bond 0.00262 (20588) covalent geometry : angle 0.57837 (27876) *********************** 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 323 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7331 (t80) REVERT: A 163 MET cc_start: 0.7688 (ttp) cc_final: 0.7428 (ttm) REVERT: A 332 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 357 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 1194 THR cc_start: 0.8206 (m) cc_final: 0.7922 (m) REVERT: A 1394 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (t) REVERT: A 1433 MET cc_start: 0.4468 (ptp) cc_final: 0.3529 (ttt) REVERT: A 1464 ARG cc_start: 0.7112 (tmt170) cc_final: 0.6794 (tpt-90) REVERT: A 1522 SER cc_start: 0.8895 (t) cc_final: 0.8424 (m) REVERT: A 1627 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: A 1732 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: A 1771 MET cc_start: 0.4339 (ptp) cc_final: 0.4085 (ppp) REVERT: D 85 ASP cc_start: 0.7669 (m-30) cc_final: 0.7148 (m-30) REVERT: D 195 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7905 (pttt) REVERT: D 601 ASP cc_start: 0.8058 (t70) cc_final: 0.7467 (m-30) REVERT: D 678 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7861 (mt-10) REVERT: D 736 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7802 (t) REVERT: D 775 PHE cc_start: 0.8570 (m-80) cc_final: 0.8275 (m-80) REVERT: D 883 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.6076 (ptp) REVERT: D 1017 MET cc_start: 0.5155 (OUTLIER) cc_final: 0.4952 (tpp) REVERT: B 247 MET cc_start: 0.5731 (tpt) cc_final: 0.4997 (mmm) outliers start: 54 outliers final: 35 residues processed: 302 average time/residue: 0.3048 time to fit residues: 145.7203 Evaluate side-chains 295 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 342 VAL 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 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 1367 THR Chi-restraints excluded: chain A residue 1394 SER Chi-restraints excluded: chain A residue 1487 MET 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 199 GLU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP 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 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 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 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4386 r_free = 0.4386 target = 0.211073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136696 restraints weight = 22245.898| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.24 r_work: 0.3422 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20616 Z= 0.126 Angle : 0.590 15.278 27949 Z= 0.296 Chirality : 0.043 0.196 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.485 106.525 3513 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.57 % Allowed : 14.69 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2414 helix: 0.06 (0.15), residues: 1241 sheet: -1.23 (0.32), residues: 257 loop : -1.21 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.015 0.001 HIS A1354 PHE 0.021 0.001 PHE A 553 TYR 0.017 0.001 TYR D 426 ARG 0.005 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 11) link_NAG-ASN : angle 2.97816 ( 33) link_BETA1-4 : bond 0.00475 ( 5) link_BETA1-4 : angle 1.59954 ( 15) hydrogen bonds : bond 0.03365 ( 869) hydrogen bonds : angle 4.37802 ( 2481) SS BOND : bond 0.00294 ( 11) SS BOND : angle 1.73113 ( 22) link_BETA1-3 : bond 0.00927 ( 1) link_BETA1-3 : angle 3.40621 ( 3) covalent geometry : bond 0.00287 (20588) covalent geometry : angle 0.57765 (27876) *********************** 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 325 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7640 (ttp) cc_final: 0.7374 (ttm) REVERT: A 332 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 357 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 472 MET cc_start: 0.5545 (ttt) cc_final: 0.5126 (ttp) REVERT: A 1156 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6190 (pt0) REVERT: A 1194 THR cc_start: 0.8170 (m) cc_final: 0.7894 (m) REVERT: A 1433 MET cc_start: 0.4557 (ptp) cc_final: 0.3670 (ttt) REVERT: A 1522 SER cc_start: 0.8810 (t) cc_final: 0.8325 (m) REVERT: A 1627 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: A 1771 MET cc_start: 0.4209 (ptp) cc_final: 0.3936 (ppp) REVERT: D 85 ASP cc_start: 0.7591 (m-30) cc_final: 0.7061 (m-30) REVERT: D 195 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7903 (pttt) REVERT: D 601 ASP cc_start: 0.8067 (t70) cc_final: 0.7504 (m-30) REVERT: D 628 PHE cc_start: 0.8319 (m-80) cc_final: 0.8035 (m-10) REVERT: D 678 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 736 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7727 (t) REVERT: D 775 PHE cc_start: 0.8554 (m-80) cc_final: 0.8257 (m-80) REVERT: D 848 MET cc_start: 0.0965 (mmt) cc_final: 0.0546 (mmm) REVERT: D 883 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6107 (ptp) REVERT: D 1042 ASN cc_start: 0.8318 (t0) cc_final: 0.8012 (t0) REVERT: B 247 MET cc_start: 0.5723 (tpt) cc_final: 0.4971 (mmm) outliers start: 55 outliers final: 41 residues processed: 304 average time/residue: 0.3100 time to fit residues: 149.8112 Evaluate side-chains 300 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL 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 1367 THR Chi-restraints excluded: chain A residue 1394 SER Chi-restraints excluded: chain A residue 1487 MET 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 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL 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 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 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 154 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 100 optimal weight: 0.0050 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** 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 246 GLN D 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.209799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135521 restraints weight = 22394.096| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.13 r_work: 0.3418 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20616 Z= 0.153 Angle : 0.609 14.178 27949 Z= 0.305 Chirality : 0.043 0.195 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.436 106.023 3513 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.48 % Allowed : 15.11 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2414 helix: 0.09 (0.15), residues: 1242 sheet: -1.27 (0.33), residues: 261 loop : -1.20 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.008 0.001 HIS A1354 PHE 0.026 0.001 PHE A1199 TYR 0.016 0.001 TYR D 426 ARG 0.013 0.000 ARG A1464 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 11) link_NAG-ASN : angle 2.98031 ( 33) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.60504 ( 15) hydrogen bonds : bond 0.03463 ( 869) hydrogen bonds : angle 4.38762 ( 2481) SS BOND : bond 0.00283 ( 11) SS BOND : angle 1.83836 ( 22) link_BETA1-3 : bond 0.00873 ( 1) link_BETA1-3 : angle 3.28442 ( 3) covalent geometry : bond 0.00363 (20588) covalent geometry : angle 0.59655 (27876) *********************** 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 307 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7714 (ttp) cc_final: 0.7410 (ttm) REVERT: A 332 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 357 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 600 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: A 1156 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6236 (pt0) REVERT: A 1194 THR cc_start: 0.8193 (m) cc_final: 0.7917 (m) REVERT: A 1433 MET cc_start: 0.4455 (ptp) cc_final: 0.3629 (ttt) REVERT: A 1464 ARG cc_start: 0.6555 (tpt90) cc_final: 0.6148 (tpt-90) REVERT: A 1522 SER cc_start: 0.8854 (t) cc_final: 0.8369 (m) REVERT: A 1627 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: A 1771 MET cc_start: 0.4278 (ptp) cc_final: 0.3975 (ppp) REVERT: A 1795 MET cc_start: 0.4265 (mtt) cc_final: 0.3575 (ppp) REVERT: D 195 LYS cc_start: 0.8256 (tmmt) cc_final: 0.7900 (pttt) REVERT: D 601 ASP cc_start: 0.8061 (t70) cc_final: 0.7461 (m-30) REVERT: D 628 PHE cc_start: 0.8308 (m-80) cc_final: 0.8068 (m-10) REVERT: D 678 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 736 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7733 (t) REVERT: D 775 PHE cc_start: 0.8569 (m-80) cc_final: 0.8228 (m-80) REVERT: D 848 MET cc_start: 0.0986 (mmt) cc_final: 0.0559 (mmm) REVERT: D 883 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6120 (ptp) REVERT: D 1042 ASN cc_start: 0.8343 (t0) cc_final: 0.8041 (t0) REVERT: B 247 MET cc_start: 0.5606 (tpt) cc_final: 0.4813 (mmm) outliers start: 53 outliers final: 41 residues processed: 287 average time/residue: 0.3130 time to fit residues: 143.5896 Evaluate side-chains 292 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 600 MET 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 1367 THR Chi-restraints excluded: chain A residue 1487 MET 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 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 109 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** 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 870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.208474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135155 restraints weight = 22392.830| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.51 r_work: 0.3367 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20616 Z= 0.190 Angle : 0.633 13.220 27949 Z= 0.318 Chirality : 0.045 0.197 3166 Planarity : 0.004 0.050 3470 Dihedral : 8.478 105.701 3513 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.12 % Rotamer: Outliers : 2.29 % Allowed : 15.30 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2414 helix: 0.07 (0.15), residues: 1239 sheet: -1.18 (0.33), residues: 258 loop : -1.22 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.007 0.001 HIS A1351 PHE 0.021 0.001 PHE A 553 TYR 0.017 0.001 TYR D 426 ARG 0.006 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 11) link_NAG-ASN : angle 3.04431 ( 33) link_BETA1-4 : bond 0.00525 ( 5) link_BETA1-4 : angle 1.59392 ( 15) hydrogen bonds : bond 0.03655 ( 869) hydrogen bonds : angle 4.43661 ( 2481) SS BOND : bond 0.00312 ( 11) SS BOND : angle 1.86476 ( 22) link_BETA1-3 : bond 0.00871 ( 1) link_BETA1-3 : angle 3.17061 ( 3) covalent geometry : bond 0.00459 (20588) covalent geometry : angle 0.62134 (27876) *********************** 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 301 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7836 (ttp) cc_final: 0.7479 (ttm) REVERT: A 332 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 357 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8619 (tm-30) REVERT: A 600 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (tpp) REVERT: A 1156 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6283 (pt0) REVERT: A 1341 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8480 (ttp) REVERT: A 1433 MET cc_start: 0.4517 (ptp) cc_final: 0.3660 (ttt) REVERT: A 1464 ARG cc_start: 0.6544 (tpt90) cc_final: 0.6103 (tpt-90) REVERT: A 1522 SER cc_start: 0.8962 (t) cc_final: 0.8511 (m) REVERT: A 1627 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: A 1771 MET cc_start: 0.4366 (ptp) cc_final: 0.4031 (ppp) REVERT: A 1795 MET cc_start: 0.4264 (mtt) cc_final: 0.3604 (ppp) REVERT: D 85 ASP cc_start: 0.7700 (m-30) cc_final: 0.7239 (m-30) REVERT: D 195 LYS cc_start: 0.8301 (tmmt) cc_final: 0.7961 (pttt) REVERT: D 452 ASP cc_start: 0.7386 (t0) cc_final: 0.7177 (t70) REVERT: D 601 ASP cc_start: 0.8114 (t70) cc_final: 0.7501 (m-30) REVERT: D 628 PHE cc_start: 0.8374 (m-80) cc_final: 0.8119 (m-10) REVERT: D 678 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 736 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7814 (t) REVERT: D 775 PHE cc_start: 0.8645 (m-80) cc_final: 0.8286 (m-80) REVERT: D 848 MET cc_start: 0.1144 (mmt) cc_final: 0.0751 (mmm) REVERT: D 883 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6208 (ptp) REVERT: D 1042 ASN cc_start: 0.8390 (t0) cc_final: 0.8087 (t0) REVERT: B 247 MET cc_start: 0.5639 (tpt) cc_final: 0.3668 (mtp) outliers start: 49 outliers final: 40 residues processed: 282 average time/residue: 0.3043 time to fit residues: 137.0063 Evaluate side-chains 296 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 600 MET 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 1341 MET Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1487 MET 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 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU 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 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 143 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** 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 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136366 restraints weight = 22281.193| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.49 r_work: 0.3377 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20616 Z= 0.172 Angle : 0.625 12.436 27949 Z= 0.313 Chirality : 0.044 0.195 3166 Planarity : 0.004 0.049 3470 Dihedral : 8.467 105.358 3513 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.34 % Allowed : 15.40 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2414 helix: 0.09 (0.15), residues: 1239 sheet: -1.16 (0.33), residues: 260 loop : -1.21 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.007 0.001 HIS A1351 PHE 0.024 0.001 PHE A 553 TYR 0.018 0.001 TYR D 426 ARG 0.006 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 11) link_NAG-ASN : angle 3.04490 ( 33) link_BETA1-4 : bond 0.00546 ( 5) link_BETA1-4 : angle 1.55857 ( 15) hydrogen bonds : bond 0.03572 ( 869) hydrogen bonds : angle 4.42682 ( 2481) SS BOND : bond 0.00337 ( 11) SS BOND : angle 2.06860 ( 22) link_BETA1-3 : bond 0.00882 ( 1) link_BETA1-3 : angle 3.08851 ( 3) covalent geometry : bond 0.00412 (20588) covalent geometry : angle 0.61256 (27876) ********************** 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 302 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7831 (ttp) cc_final: 0.7465 (ttm) REVERT: A 332 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 357 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 600 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8164 (tpp) REVERT: A 1156 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6281 (pt0) REVERT: A 1341 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8473 (ttp) REVERT: A 1433 MET cc_start: 0.4497 (ptp) cc_final: 0.3559 (ttt) REVERT: A 1464 ARG cc_start: 0.6528 (tpt90) cc_final: 0.6061 (tpt-90) REVERT: A 1627 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: A 1771 MET cc_start: 0.4449 (ptp) cc_final: 0.4116 (ppp) REVERT: A 1795 MET cc_start: 0.4210 (mtt) cc_final: 0.3574 (ppp) REVERT: D 85 ASP cc_start: 0.7699 (m-30) cc_final: 0.7261 (m-30) REVERT: D 195 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7948 (pttt) REVERT: D 452 ASP cc_start: 0.7354 (t0) cc_final: 0.7150 (t70) REVERT: D 601 ASP cc_start: 0.8115 (t70) cc_final: 0.7506 (m-30) REVERT: D 628 PHE cc_start: 0.8366 (m-80) cc_final: 0.8099 (m-10) REVERT: D 678 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 736 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.7869 (t) REVERT: D 848 MET cc_start: 0.1011 (mmt) cc_final: 0.0643 (mmm) REVERT: D 883 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6191 (ptp) REVERT: B 247 MET cc_start: 0.5628 (tpt) cc_final: 0.3663 (mtp) outliers start: 50 outliers final: 42 residues processed: 282 average time/residue: 0.3165 time to fit residues: 143.3944 Evaluate side-chains 295 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 600 MET 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 1341 MET Chi-restraints excluded: chain A residue 1354 HIS Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 SER Chi-restraints excluded: chain A residue 1487 MET 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 1739 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU 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 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 170 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 203 optimal weight: 0.0870 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.210100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136201 restraints weight = 22331.111| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.34 r_work: 0.3399 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20616 Z= 0.136 Angle : 0.597 11.702 27949 Z= 0.300 Chirality : 0.043 0.190 3166 Planarity : 0.004 0.049 3470 Dihedral : 8.402 105.656 3513 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.29 % Allowed : 15.77 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2414 helix: 0.20 (0.15), residues: 1242 sheet: -1.11 (0.33), residues: 260 loop : -1.17 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.005 0.001 HIS A1354 PHE 0.023 0.001 PHE A 553 TYR 0.018 0.001 TYR D 744 ARG 0.006 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 11) link_NAG-ASN : angle 2.97635 ( 33) link_BETA1-4 : bond 0.00560 ( 5) link_BETA1-4 : angle 1.49662 ( 15) hydrogen bonds : bond 0.03372 ( 869) hydrogen bonds : angle 4.35234 ( 2481) SS BOND : bond 0.00245 ( 11) SS BOND : angle 1.86289 ( 22) link_BETA1-3 : bond 0.00894 ( 1) link_BETA1-3 : angle 3.04782 ( 3) covalent geometry : bond 0.00317 (20588) covalent geometry : angle 0.58481 (27876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14641.12 seconds wall clock time: 249 minutes 46.33 seconds (14986.33 seconds total)