Starting phenix.real_space_refine on Wed May 21 11:58:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg5_33808/05_2025/7yg5_33808_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.093 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 2 5.49 5 S 113 5.16 5 C 13223 2.51 5 N 3276 2.21 5 O 3692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20308 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: {'PTRANS': 40, 'TRANS': 1278} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1269 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 6 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: "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: "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: "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: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 498 Unusual residues: {' CA': 1, '3PE': 2, 'R16': 6, 'TOR': 1, 'Y01': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 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 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N 3PE A2404 " occ=0.00 ... (38 atoms not shown) pdb=" P 3PE A2404 " occ=0.00 residue: pdb=" N 3PE A2405 " occ=0.00 ... (38 atoms not shown) pdb=" P 3PE A2405 " occ=0.00 Time building chain proxies: 11.06, per 1000 atoms: 0.54 Number of scatterers: 20308 At special positions: 0 Unit cell: (175.76, 113.36, 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 113 16.00 P 2 15.00 O 3692 8.00 N 3276 7.00 C 13223 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=2.03 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=2.02 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=2.04 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 468 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 324 " " NAG D1204 " - " ASN D 348 " " NAG D1205 " - " ASN D 604 " " NAG D1206 " - " ASN D 613 " " NAG D1207 " - " ASN D 675 " " NAG D1208 " - " ASN D 888 " " NAG D1209 " - " ASN D 184 " " NAG E 1 " - " ASN D 895 " " NAG F 1 " - " ASN D 824 " Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.3 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: 106 helices and 17 sheets defined 53.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.514A pdb=" N GLU A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 127 through 145 Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.866A pdb=" N VAL A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.749A pdb=" N VAL A 194 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 204 through 218 removed outlier: 4.270A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 222 Processing helix chain 'A' and resid 223 through 243 removed outlier: 3.507A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.639A pdb=" N PHE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.921A pdb=" N VAL A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 360 through 385 removed outlier: 3.779A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.912A pdb=" N LEU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 467 through 473 removed outlier: 3.509A pdb=" N HIS A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 removed outlier: 3.761A pdb=" N TRP A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.665A pdb=" N HIS A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 560 Processing helix chain 'A' and resid 569 through 583 Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.588A pdb=" N LEU A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 626 removed outlier: 3.946A pdb=" N LEU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 removed outlier: 3.726A pdb=" N MET A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.715A pdb=" N VAL A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 682 removed outlier: 3.568A pdb=" N SER A 679 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 681 " --> pdb=" O TRP A 678 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 682 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.565A pdb=" N ALA A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 776 through 788 Processing helix chain 'A' and resid 1146 through 1151 removed outlier: 3.929A pdb=" N ASN A1151 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1172 removed outlier: 3.767A pdb=" N LEU A1161 " --> pdb=" O MET A1157 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1209 removed outlier: 3.621A pdb=" N LYS A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1242 Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.569A 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: 3.816A pdb=" N ARG A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1289 Processing helix chain 'A' and resid 1292 through 1312 Processing helix chain 'A' and resid 1357 through 1370 removed outlier: 3.570A pdb=" N VAL A1368 " --> pdb=" O THR A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1383 removed outlier: 3.619A pdb=" N VAL A1377 " --> pdb=" O GLY A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1400 removed outlier: 3.546A pdb=" N SER A1400 " --> pdb=" O MET A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 3.921A pdb=" N PHE A1407 " --> pdb=" O TYR A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1425 removed outlier: 3.699A pdb=" N ASN A1416 " --> pdb=" O PHE A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 removed outlier: 3.660A pdb=" N SER A1438 " --> pdb=" O MET A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1447 Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1470 through 1476 Processing helix chain 'A' and resid 1480 through 1495 removed outlier: 4.163A pdb=" N VAL A1493 " --> pdb=" O ALA A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1526 Processing helix chain 'A' and resid 1528 through 1533 Processing helix chain 'A' and resid 1533 through 1538 removed outlier: 3.559A pdb=" N PHE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1561 removed outlier: 3.606A pdb=" N ASP A1561 " --> pdb=" O ILE A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 4.158A pdb=" N PHE A1578 " --> pdb=" O PHE A1574 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 3.656A pdb=" N ARG A1588 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A1589 " --> pdb=" O LYS A1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1584 through 1589' Processing helix chain 'A' and resid 1592 through 1606 removed outlier: 3.548A pdb=" N LEU A1596 " --> pdb=" O THR A1592 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A1604 " --> pdb=" O PHE A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1630 removed outlier: 3.811A pdb=" N ILE A1614 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A1615 " --> pdb=" O CYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1661 Processing helix chain 'A' and resid 1664 through 1672 Processing helix chain 'A' and resid 1698 through 1723 removed outlier: 3.534A pdb=" N PHE A1706 " --> pdb=" O TYR A1702 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A1715 " --> pdb=" O SER A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1730 Processing helix chain 'A' and resid 1737 through 1742 removed outlier: 3.821A pdb=" N LEU A1741 " --> pdb=" O GLY A1737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A1742 " --> pdb=" O PRO A1738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1737 through 1742' Processing helix chain 'A' and resid 1742 through 1752 Processing helix chain 'A' and resid 1761 through 1768 removed outlier: 3.624A pdb=" N TYR A1765 " --> pdb=" O TYR A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1791 Processing helix chain 'A' and resid 1804 through 1818 removed outlier: 3.678A pdb=" N THR A1808 " --> pdb=" O HIS A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1843 removed outlier: 3.633A pdb=" N GLN A1829 " --> pdb=" O GLY A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1855 Processing helix chain 'B' and resid 242 through 260 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 303 through 314 removed outlier: 4.438A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 removed outlier: 3.594A pdb=" N LEU B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 333 " --> pdb=" O ALA B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 333' Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.905A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 6.223A pdb=" N GLU B 383 " --> pdb=" O CYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 412 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 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.637A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.583A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 376 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.712A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 431 removed outlier: 3.849A pdb=" N ASN D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.755A pdb=" N VAL D 572 " --> pdb=" O ASN D 568 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 690 through 694 Processing helix chain 'D' and resid 698 through 719 removed outlier: 3.984A 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: 3.510A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 890 removed outlier: 3.872A pdb=" N MET D 883 " --> pdb=" O ASP D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1047 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 'B' and resid 232 through 235 removed outlier: 7.142A pdb=" N ILE B 233 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 344 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 235 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 341 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 389 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B 343 " --> pdb=" O LEU B 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 264 through 268 Processing sheet with id=AA6, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA7, first strand: chain 'D' and resid 143 through 144 removed outlier: 9.049A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 143 through 144 removed outlier: 9.049A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'D' and resid 298 through 300 removed outlier: 5.816A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR D 409 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 288 through 289 Processing sheet with id=AB3, first strand: chain 'D' and resid 521 through 523 removed outlier: 3.693A pdb=" N LEU D 523 " --> pdb=" O ALA D 514 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 591 through 593 Processing sheet with id=AB5, first strand: chain 'D' and resid 729 through 736 removed outlier: 3.674A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 800 through 802 Processing sheet with id=AB7, first strand: chain 'D' and resid 861 through 862 removed outlier: 3.870A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 892 through 904 removed outlier: 5.418A pdb=" N PHE D 894 " --> pdb=" O PHE D 982 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE D 982 " --> pdb=" O PHE D 894 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS D 896 " --> pdb=" O GLN D 980 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLN D 980 " --> pdb=" O LYS D 896 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR D 898 " --> pdb=" O GLN D 978 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN D 978 " --> pdb=" O TYR D 898 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR D 900 " --> pdb=" O THR D 976 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR D 976 " --> pdb=" O TYR D 900 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2622 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: 7.94 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2873 1.25 - 1.39: 5457 1.39 - 1.53: 11709 1.53 - 1.68: 553 1.68 - 1.82: 183 Bond restraints: 20775 Sorted by residual: bond pdb=" CAK TOR A2416 " pdb=" CAL TOR A2416 " ideal model delta sigma weight residual 1.544 1.109 0.435 2.00e-02 2.50e+03 4.73e+02 bond pdb=" CAB TOR A2416 " pdb=" CAG TOR A2416 " ideal model delta sigma weight residual 1.526 1.187 0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" CAU TOR A2416 " pdb=" OAQ TOR A2416 " ideal model delta sigma weight residual 1.419 1.102 0.317 2.00e-02 2.50e+03 2.51e+02 bond pdb=" CAL TOR A2416 " pdb=" OAR TOR A2416 " ideal model delta sigma weight residual 1.401 1.161 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" CAB TOR A2416 " pdb=" OAA TOR A2416 " ideal model delta sigma weight residual 1.409 1.637 -0.228 2.00e-02 2.50e+03 1.29e+02 ... (remaining 20770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27066 2.49 - 4.97: 918 4.97 - 7.46: 127 7.46 - 9.94: 30 9.94 - 12.43: 7 Bond angle restraints: 28148 Sorted by residual: angle pdb=" N HIS A1351 " pdb=" CA HIS A1351 " pdb=" C HIS A1351 " ideal model delta sigma weight residual 110.53 98.10 12.43 1.29e+00 6.01e-01 9.29e+01 angle pdb=" N PRO A 89 " pdb=" CA PRO A 89 " pdb=" C PRO A 89 " ideal model delta sigma weight residual 110.70 119.69 -8.99 1.22e+00 6.72e-01 5.43e+01 angle pdb=" N GLU A 92 " pdb=" CA GLU A 92 " pdb=" C GLU A 92 " ideal model delta sigma weight residual 113.97 105.00 8.97 1.28e+00 6.10e-01 4.91e+01 angle pdb=" C ASP A1356 " pdb=" CA ASP A1356 " pdb=" CB ASP A1356 " ideal model delta sigma weight residual 110.72 98.92 11.80 1.69e+00 3.50e-01 4.87e+01 angle pdb=" N TYR A 682 " pdb=" CA TYR A 682 " pdb=" C TYR A 682 " ideal model delta sigma weight residual 112.90 103.77 9.13 1.31e+00 5.83e-01 4.86e+01 ... (remaining 28143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 12175 25.03 - 50.06: 774 50.06 - 75.09: 127 75.09 - 100.11: 35 100.11 - 125.14: 24 Dihedral angle restraints: 13135 sinusoidal: 6002 harmonic: 7133 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 8.63 84.37 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual -86.00 -14.19 -71.81 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS D 999 " pdb=" SG CYS D 999 " pdb=" SG CYS D1024 " pdb=" CB CYS D1024 " ideal model delta sinusoidal sigma weight residual 93.00 156.42 -63.42 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 13132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 3182 0.234 - 0.469: 15 0.469 - 0.703: 1 0.703 - 0.937: 0 0.937 - 1.172: 1 Chirality restraints: 3199 Sorted by residual: chirality pdb=" CAL TOR A2416 " pdb=" CAK TOR A2416 " pdb=" OAH TOR A2416 " pdb=" OAR TOR A2416 " both_signs ideal model delta sigma weight residual False -2.23 -1.06 -1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CAK TOR A2416 " pdb=" CAG TOR A2416 " pdb=" CAL TOR A2416 " pdb=" OAQ TOR A2416 " both_signs ideal model delta sigma weight residual False -2.47 -1.95 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CAB TOR A2416 " pdb=" CAC TOR A2416 " pdb=" CAG TOR A2416 " pdb=" OAA TOR A2416 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 3196 not shown) Planarity restraints: 3490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 516 " 0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO D 517 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 517 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 517 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1773 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A1774 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A1774 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1774 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 266 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO A 267 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.036 5.00e-02 4.00e+02 ... (remaining 3487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2879 2.74 - 3.28: 20612 3.28 - 3.82: 32841 3.82 - 4.36: 41055 4.36 - 4.90: 69027 Nonbonded interactions: 166414 Sorted by model distance: nonbonded pdb=" NZ LYS D 442 " pdb=" O PRO D 465 " model vdw 2.195 3.120 nonbonded pdb=" OG SER D 594 " pdb=" OD1 ASP D 596 " model vdw 2.206 3.040 nonbonded pdb=" OD2 ASP A1324 " pdb=" NH2 ARG A1389 " model vdw 2.221 3.120 nonbonded pdb=" O LEU D 506 " pdb=" OH TYR D 759 " model vdw 2.222 3.040 nonbonded pdb=" O ASN D 295 " pdb=" OG SER D 296 " model vdw 2.227 3.040 ... (remaining 166409 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=0.00 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: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.780 Find NCS groups from input model: 0.430 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.015 0.435 20803 Z= 0.673 Angle : 1.103 12.431 28221 Z= 0.608 Chirality : 0.069 1.172 3199 Planarity : 0.006 0.104 3479 Dihedral : 17.207 125.143 8492 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.85 % Favored : 88.82 % Rotamer: Outliers : 0.56 % Allowed : 1.21 % Favored : 98.23 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2414 helix: -1.41 (0.14), residues: 1195 sheet: -1.37 (0.34), residues: 233 loop : -2.29 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 88 HIS 0.010 0.002 HIS D 864 PHE 0.035 0.003 PHE A1303 TYR 0.029 0.003 TYR D1068 ARG 0.015 0.001 ARG A 668 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 11) link_NAG-ASN : angle 3.74064 ( 33) link_BETA1-4 : bond 0.00604 ( 5) link_BETA1-4 : angle 2.48427 ( 15) hydrogen bonds : bond 0.15709 ( 923) hydrogen bonds : angle 7.29509 ( 2622) SS BOND : bond 0.00424 ( 11) SS BOND : angle 3.67571 ( 22) link_BETA1-3 : bond 0.00539 ( 1) link_BETA1-3 : angle 5.52302 ( 3) covalent geometry : bond 0.01500 (20775) covalent geometry : angle 1.08894 (28148) *********************** 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 290 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8500 (tp30) cc_final: 0.8047 (tp30) REVERT: A 377 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 1591 TYR cc_start: 0.7606 (t80) cc_final: 0.7118 (t80) REVERT: A 1793 MET cc_start: 0.6468 (ppp) cc_final: 0.5723 (ppp) REVERT: A 1810 MET cc_start: 0.8029 (mmt) cc_final: 0.7793 (mpp) REVERT: B 249 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7253 (mm-40) REVERT: B 354 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7632 (mtt180) REVERT: D 64 TYR cc_start: 0.7899 (m-80) cc_final: 0.7095 (m-80) REVERT: D 284 SER cc_start: 0.8662 (p) cc_final: 0.8424 (m) REVERT: D 366 GLU cc_start: 0.6433 (tt0) cc_final: 0.6170 (tm-30) REVERT: D 653 PHE cc_start: 0.6875 (m-80) cc_final: 0.6653 (m-10) REVERT: D 750 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7512 (mp0) REVERT: D 977 GLU cc_start: 0.8071 (tp30) cc_final: 0.7757 (tm-30) outliers start: 12 outliers final: 7 residues processed: 287 average time/residue: 1.1441 time to fit residues: 380.5259 Evaluate side-chains 234 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 1760 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 0.0670 chunk 97 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 294 ASN A 623 GLN A 696 ASN A 727 HIS A1291 ASN A1602 GLN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN D 509 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 717 GLN D 864 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117336 restraints weight = 26826.625| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.43 r_work: 0.3249 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20803 Z= 0.149 Angle : 0.722 13.589 28221 Z= 0.364 Chirality : 0.046 0.292 3199 Planarity : 0.005 0.080 3479 Dihedral : 12.586 104.241 3822 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 1.49 % Allowed : 9.99 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -1.60 (0.17), residues: 2414 helix: -0.34 (0.15), residues: 1176 sheet: -1.67 (0.32), residues: 236 loop : -1.69 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 185 HIS 0.005 0.001 HIS A 183 PHE 0.022 0.001 PHE A1449 TYR 0.032 0.002 TYR D 426 ARG 0.006 0.001 ARG A1693 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 11) link_NAG-ASN : angle 3.61961 ( 33) link_BETA1-4 : bond 0.00680 ( 5) link_BETA1-4 : angle 2.46698 ( 15) hydrogen bonds : bond 0.04347 ( 923) hydrogen bonds : angle 5.11478 ( 2622) SS BOND : bond 0.00462 ( 11) SS BOND : angle 2.37788 ( 22) link_BETA1-3 : bond 0.00770 ( 1) link_BETA1-3 : angle 4.99187 ( 3) covalent geometry : bond 0.00328 (20775) covalent geometry : angle 0.70502 (28148) *********************** 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 302 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8768 (tp30) cc_final: 0.8053 (tp30) REVERT: A 128 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 373 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 377 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7290 (mp0) REVERT: A 1157 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7148 (tmt) REVERT: A 1167 SER cc_start: 0.9099 (m) cc_final: 0.8870 (m) REVERT: A 1205 MET cc_start: 0.4993 (mmt) cc_final: 0.4791 (mpp) REVERT: A 1387 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8203 (tt0) REVERT: A 1434 MET cc_start: 0.4137 (ttp) cc_final: 0.3843 (ttp) REVERT: A 1462 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.6017 (pp30) REVERT: A 1467 PHE cc_start: 0.6717 (p90) cc_final: 0.5851 (p90) REVERT: A 1591 TYR cc_start: 0.7993 (t80) cc_final: 0.7427 (t80) REVERT: A 1793 MET cc_start: 0.6274 (ppp) cc_final: 0.5764 (ppp) REVERT: A 1810 MET cc_start: 0.7815 (mmt) cc_final: 0.7580 (mpp) REVERT: D 64 TYR cc_start: 0.8131 (m-80) cc_final: 0.7017 (m-80) REVERT: D 246 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8554 (tm-30) REVERT: D 366 GLU cc_start: 0.7288 (tt0) cc_final: 0.6776 (mm-30) REVERT: D 428 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7252 (t0) REVERT: D 516 ASP cc_start: 0.8396 (t0) cc_final: 0.8045 (t0) REVERT: D 526 ASN cc_start: 0.9004 (t0) cc_final: 0.8652 (t0) REVERT: D 653 PHE cc_start: 0.6950 (m-80) cc_final: 0.6084 (m-80) REVERT: D 744 TYR cc_start: 0.7281 (t80) cc_final: 0.7024 (t80) REVERT: D 848 MET cc_start: 0.1655 (OUTLIER) cc_final: 0.1283 (mmt) REVERT: D 892 TYR cc_start: 0.8278 (m-10) cc_final: 0.8026 (m-10) REVERT: D 977 GLU cc_start: 0.8044 (tp30) cc_final: 0.7461 (tm-30) outliers start: 32 outliers final: 8 residues processed: 282 average time/residue: 1.0839 time to fit residues: 354.2221 Evaluate side-chains 245 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 848 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 192 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 237 optimal weight: 40.0000 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1589 GLN A1602 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 864 HIS D 870 GLN D 980 GLN D 985 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118367 restraints weight = 26800.837| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.42 r_work: 0.3258 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 20803 Z= 0.141 Angle : 0.666 13.461 28221 Z= 0.334 Chirality : 0.044 0.250 3199 Planarity : 0.004 0.076 3479 Dihedral : 11.134 103.786 3808 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.83 % Favored : 92.13 % Rotamer: Outliers : 2.15 % Allowed : 13.12 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.17), residues: 2414 helix: 0.02 (0.15), residues: 1185 sheet: -1.80 (0.33), residues: 222 loop : -1.55 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1472 HIS 0.005 0.001 HIS A1760 PHE 0.020 0.001 PHE A1449 TYR 0.012 0.001 TYR A1765 ARG 0.007 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 11) link_NAG-ASN : angle 3.44683 ( 33) link_BETA1-4 : bond 0.00695 ( 5) link_BETA1-4 : angle 2.48700 ( 15) hydrogen bonds : bond 0.03936 ( 923) hydrogen bonds : angle 4.80471 ( 2622) SS BOND : bond 0.00284 ( 11) SS BOND : angle 2.01775 ( 22) link_BETA1-3 : bond 0.00864 ( 1) link_BETA1-3 : angle 4.88950 ( 3) covalent geometry : bond 0.00327 (20775) covalent geometry : angle 0.64938 (28148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8654 (tp30) cc_final: 0.7998 (tp30) REVERT: A 128 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 373 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 1167 SER cc_start: 0.9101 (m) cc_final: 0.8869 (m) REVERT: A 1205 MET cc_start: 0.5152 (mmt) cc_final: 0.4951 (mpp) REVERT: A 1387 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8165 (tt0) REVERT: A 1434 MET cc_start: 0.3961 (ttp) cc_final: 0.3745 (ttp) REVERT: A 1591 TYR cc_start: 0.8000 (t80) cc_final: 0.7478 (t80) REVERT: A 1793 MET cc_start: 0.6222 (ppp) cc_final: 0.5767 (ppp) REVERT: A 1810 MET cc_start: 0.7889 (mmt) cc_final: 0.7631 (mpp) REVERT: B 391 GLU cc_start: 0.7468 (pt0) cc_final: 0.7237 (pt0) REVERT: D 64 TYR cc_start: 0.8169 (m-80) cc_final: 0.7108 (m-80) REVERT: D 246 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8524 (tm-30) REVERT: D 366 GLU cc_start: 0.7281 (tt0) cc_final: 0.6820 (mm-30) REVERT: D 526 ASN cc_start: 0.8992 (t0) cc_final: 0.8701 (t0) REVERT: D 653 PHE cc_start: 0.6935 (m-80) cc_final: 0.6164 (m-80) REVERT: D 686 PHE cc_start: 0.7991 (m-80) cc_final: 0.7633 (m-80) REVERT: D 744 TYR cc_start: 0.7329 (t80) cc_final: 0.7019 (t80) REVERT: D 772 ASN cc_start: 0.7172 (p0) cc_final: 0.6872 (p0) REVERT: D 848 MET cc_start: 0.1635 (OUTLIER) cc_final: 0.1297 (tpt) REVERT: D 870 GLN cc_start: 0.7489 (pt0) cc_final: 0.7071 (pp30) REVERT: D 892 TYR cc_start: 0.8205 (m-10) cc_final: 0.7851 (m-10) REVERT: D 977 GLU cc_start: 0.7888 (tp30) cc_final: 0.7450 (tm-30) outliers start: 46 outliers final: 18 residues processed: 283 average time/residue: 1.0948 time to fit residues: 359.7333 Evaluate side-chains 255 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 114 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 727 HIS A 774 HIS A1589 GLN A1725 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 980 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.180999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122202 restraints weight = 27124.157| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.53 r_work: 0.3279 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 20803 Z= 0.130 Angle : 0.638 13.422 28221 Z= 0.321 Chirality : 0.044 0.230 3199 Planarity : 0.004 0.077 3479 Dihedral : 10.009 102.427 3808 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.05 % Allowed : 15.69 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.17), residues: 2414 helix: 0.31 (0.15), residues: 1192 sheet: -1.73 (0.33), residues: 220 loop : -1.49 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.010 0.001 HIS A1760 PHE 0.018 0.001 PHE D 780 TYR 0.028 0.001 TYR D 426 ARG 0.009 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 11) link_NAG-ASN : angle 3.37952 ( 33) link_BETA1-4 : bond 0.00681 ( 5) link_BETA1-4 : angle 2.47440 ( 15) hydrogen bonds : bond 0.03598 ( 923) hydrogen bonds : angle 4.56040 ( 2622) SS BOND : bond 0.00327 ( 11) SS BOND : angle 2.04627 ( 22) link_BETA1-3 : bond 0.00662 ( 1) link_BETA1-3 : angle 4.54929 ( 3) covalent geometry : bond 0.00301 (20775) covalent geometry : angle 0.62124 (28148) *********************** 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 302 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8593 (tp30) cc_final: 0.8063 (tp30) REVERT: A 125 GLU cc_start: 0.8490 (tp30) cc_final: 0.8286 (mm-30) REVERT: A 138 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6636 (tt0) REVERT: A 365 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8069 (ptp-110) REVERT: A 373 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 530 MET cc_start: 0.7402 (tmm) cc_final: 0.6826 (tmt) REVERT: A 1157 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7235 (tmt) REVERT: A 1167 SER cc_start: 0.9118 (m) cc_final: 0.8910 (m) REVERT: A 1205 MET cc_start: 0.5201 (mmt) cc_final: 0.4950 (mpp) REVERT: A 1429 GLN cc_start: 0.6365 (mp10) cc_final: 0.5862 (pp30) REVERT: A 1470 ARG cc_start: 0.7134 (tpt-90) cc_final: 0.6876 (mmm-85) REVERT: A 1472 TRP cc_start: 0.7460 (t60) cc_final: 0.7049 (t60) REVERT: A 1793 MET cc_start: 0.6257 (ppp) cc_final: 0.5847 (ppp) REVERT: B 391 GLU cc_start: 0.7564 (pt0) cc_final: 0.7354 (pt0) REVERT: B 405 LEU cc_start: 0.5631 (mm) cc_final: 0.5100 (pp) REVERT: D 64 TYR cc_start: 0.8125 (m-80) cc_final: 0.7139 (m-80) REVERT: D 191 GLU cc_start: 0.8049 (pp20) cc_final: 0.7762 (pp20) REVERT: D 246 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 366 GLU cc_start: 0.7274 (tt0) cc_final: 0.6865 (mm-30) REVERT: D 526 ASN cc_start: 0.8995 (t0) cc_final: 0.8673 (t0) REVERT: D 589 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7910 (mtp85) REVERT: D 653 PHE cc_start: 0.6858 (m-80) cc_final: 0.6205 (m-80) REVERT: D 744 TYR cc_start: 0.7378 (t80) cc_final: 0.7137 (t80) REVERT: D 772 ASN cc_start: 0.7185 (p0) cc_final: 0.6860 (p0) REVERT: D 848 MET cc_start: 0.1429 (OUTLIER) cc_final: 0.1015 (tpt) REVERT: D 861 MET cc_start: 0.6609 (pmm) cc_final: 0.6282 (pmm) REVERT: D 870 GLN cc_start: 0.7505 (pt0) cc_final: 0.7169 (pp30) REVERT: D 980 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8172 (mm110) REVERT: D 1036 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7161 (tt0) outliers start: 44 outliers final: 22 residues processed: 285 average time/residue: 1.1177 time to fit residues: 370.0295 Evaluate side-chains 258 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 980 GLN Chi-restraints excluded: chain D residue 1036 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 222 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 163 optimal weight: 0.5980 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 727 HIS A1589 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** 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 = 0.4154 r_free = 0.4154 target = 0.181526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122754 restraints weight = 27049.098| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.49 r_work: 0.3283 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 20803 Z= 0.124 Angle : 0.620 13.310 28221 Z= 0.311 Chirality : 0.044 0.221 3199 Planarity : 0.004 0.078 3479 Dihedral : 9.482 101.923 3808 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.15 % Allowed : 17.13 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.18), residues: 2414 helix: 0.52 (0.15), residues: 1190 sheet: -1.56 (0.33), residues: 234 loop : -1.41 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 PHE 0.021 0.001 PHE D 780 TYR 0.016 0.001 TYR A1765 ARG 0.006 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 11) link_NAG-ASN : angle 3.28462 ( 33) link_BETA1-4 : bond 0.00623 ( 5) link_BETA1-4 : angle 2.25921 ( 15) hydrogen bonds : bond 0.03456 ( 923) hydrogen bonds : angle 4.46191 ( 2622) SS BOND : bond 0.00151 ( 11) SS BOND : angle 1.64157 ( 22) link_BETA1-3 : bond 0.00825 ( 1) link_BETA1-3 : angle 4.11048 ( 3) covalent geometry : bond 0.00289 (20775) covalent geometry : angle 0.60527 (28148) *********************** 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 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8456 (tp30) cc_final: 0.8238 (mm-30) REVERT: A 215 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6331 (tmt) REVERT: A 365 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8141 (ptp-110) REVERT: A 373 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 530 MET cc_start: 0.7364 (tmm) cc_final: 0.7134 (tmt) REVERT: A 568 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 1156 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7076 (pm20) REVERT: A 1167 SER cc_start: 0.9121 (m) cc_final: 0.8912 (m) REVERT: A 1205 MET cc_start: 0.5323 (mmt) cc_final: 0.5058 (mpp) REVERT: A 1429 GLN cc_start: 0.6442 (mp10) cc_final: 0.5832 (pp30) REVERT: A 1433 MET cc_start: 0.4482 (ppp) cc_final: 0.1931 (mmm) REVERT: A 1470 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6811 (mmm-85) REVERT: A 1793 MET cc_start: 0.6216 (ppp) cc_final: 0.5810 (ppp) REVERT: A 1836 GLN cc_start: 0.7439 (tp-100) cc_final: 0.6731 (mt0) REVERT: B 357 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7690 (mmtm) REVERT: B 405 LEU cc_start: 0.5586 (mm) cc_final: 0.5068 (pp) REVERT: D 64 TYR cc_start: 0.8115 (m-80) cc_final: 0.7117 (m-80) REVERT: D 102 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8539 (mm) REVERT: D 366 GLU cc_start: 0.7251 (tt0) cc_final: 0.6875 (mm-30) REVERT: D 526 ASN cc_start: 0.8993 (t0) cc_final: 0.8667 (t0) REVERT: D 589 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7851 (mtp85) REVERT: D 653 PHE cc_start: 0.6847 (m-80) cc_final: 0.6229 (m-80) REVERT: D 744 TYR cc_start: 0.7386 (t80) cc_final: 0.7151 (t80) REVERT: D 772 ASN cc_start: 0.7109 (p0) cc_final: 0.6786 (p0) REVERT: D 848 MET cc_start: 0.1460 (OUTLIER) cc_final: 0.1125 (tpt) REVERT: D 861 MET cc_start: 0.6595 (pmm) cc_final: 0.6287 (pmm) REVERT: D 870 GLN cc_start: 0.7477 (pt0) cc_final: 0.7137 (pp30) REVERT: D 1036 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7084 (tt0) outliers start: 46 outliers final: 20 residues processed: 285 average time/residue: 1.0632 time to fit residues: 352.4672 Evaluate side-chains 264 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1470 ARG Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 1036 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 201 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A 774 HIS A1589 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** 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 = 0.4159 r_free = 0.4159 target = 0.182038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122611 restraints weight = 27006.556| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.51 r_work: 0.3294 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20803 Z= 0.122 Angle : 0.605 13.245 28221 Z= 0.304 Chirality : 0.043 0.218 3199 Planarity : 0.004 0.079 3479 Dihedral : 9.187 101.309 3808 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.33 % Allowed : 18.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.18), residues: 2414 helix: 0.65 (0.15), residues: 1205 sheet: -1.57 (0.33), residues: 236 loop : -1.32 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 PHE 0.024 0.001 PHE D 780 TYR 0.026 0.001 TYR D 426 ARG 0.006 0.000 ARG D 766 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 11) link_NAG-ASN : angle 3.23973 ( 33) link_BETA1-4 : bond 0.00605 ( 5) link_BETA1-4 : angle 2.07212 ( 15) hydrogen bonds : bond 0.03374 ( 923) hydrogen bonds : angle 4.37074 ( 2622) SS BOND : bond 0.00147 ( 11) SS BOND : angle 1.26058 ( 22) link_BETA1-3 : bond 0.00862 ( 1) link_BETA1-3 : angle 3.84121 ( 3) covalent geometry : bond 0.00283 (20775) covalent geometry : angle 0.59150 (28148) *********************** 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 312 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: A 215 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6363 (tmt) REVERT: A 365 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8116 (ptp-110) REVERT: A 373 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 530 MET cc_start: 0.7355 (tmm) cc_final: 0.7116 (tmt) REVERT: A 584 LYS cc_start: 0.8366 (pttm) cc_final: 0.7530 (pmmt) REVERT: A 1156 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7041 (pm20) REVERT: A 1167 SER cc_start: 0.9056 (m) cc_final: 0.8811 (m) REVERT: A 1205 MET cc_start: 0.5321 (mmt) cc_final: 0.5065 (mpp) REVERT: A 1429 GLN cc_start: 0.6441 (mp10) cc_final: 0.5786 (pp30) REVERT: A 1472 TRP cc_start: 0.7404 (t60) cc_final: 0.6668 (t-100) REVERT: A 1504 CYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5695 (m) REVERT: A 1793 MET cc_start: 0.6311 (ppp) cc_final: 0.5905 (ppp) REVERT: A 1836 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6537 (mt0) REVERT: B 357 LYS cc_start: 0.7969 (mppt) cc_final: 0.7712 (mmtm) REVERT: B 367 LEU cc_start: 0.7295 (tm) cc_final: 0.6977 (mt) REVERT: B 389 LEU cc_start: 0.6033 (mt) cc_final: 0.5729 (tt) REVERT: B 391 GLU cc_start: 0.7485 (pt0) cc_final: 0.7133 (pt0) REVERT: B 405 LEU cc_start: 0.5781 (mm) cc_final: 0.5312 (pp) REVERT: D 64 TYR cc_start: 0.8029 (m-80) cc_final: 0.7034 (m-80) REVERT: D 102 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 191 GLU cc_start: 0.8074 (pp20) cc_final: 0.7865 (pp20) REVERT: D 366 GLU cc_start: 0.7138 (tt0) cc_final: 0.6805 (mm-30) REVERT: D 526 ASN cc_start: 0.9001 (t0) cc_final: 0.8669 (t0) REVERT: D 589 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7745 (mtp85) REVERT: D 653 PHE cc_start: 0.6723 (m-80) cc_final: 0.6095 (m-80) REVERT: D 678 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8643 (tm-30) REVERT: D 744 TYR cc_start: 0.7420 (t80) cc_final: 0.7212 (t80) REVERT: D 772 ASN cc_start: 0.7130 (p0) cc_final: 0.6823 (p0) REVERT: D 848 MET cc_start: 0.1530 (mmp) cc_final: 0.1189 (tpt) REVERT: D 861 MET cc_start: 0.6476 (pmm) cc_final: 0.6211 (pmm) REVERT: D 870 GLN cc_start: 0.7614 (pt0) cc_final: 0.7242 (pp30) outliers start: 50 outliers final: 22 residues processed: 294 average time/residue: 1.0654 time to fit residues: 366.8841 Evaluate side-chains 272 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 979 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 70 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 124 optimal weight: 0.0870 chunk 229 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1589 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.181446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119876 restraints weight = 27021.317| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.20 r_work: 0.3284 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 20803 Z= 0.138 Angle : 0.625 13.183 28221 Z= 0.311 Chirality : 0.044 0.221 3199 Planarity : 0.004 0.080 3479 Dihedral : 9.094 101.549 3808 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.43 % Allowed : 19.14 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.18), residues: 2414 helix: 0.69 (0.15), residues: 1212 sheet: -1.46 (0.33), residues: 234 loop : -1.31 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 PHE 0.027 0.001 PHE D 780 TYR 0.016 0.001 TYR A1765 ARG 0.008 0.000 ARG B 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 11) link_NAG-ASN : angle 3.20158 ( 33) link_BETA1-4 : bond 0.00641 ( 5) link_BETA1-4 : angle 1.94707 ( 15) hydrogen bonds : bond 0.03422 ( 923) hydrogen bonds : angle 4.35464 ( 2622) SS BOND : bond 0.00160 ( 11) SS BOND : angle 1.21439 ( 22) link_BETA1-3 : bond 0.00814 ( 1) link_BETA1-3 : angle 3.75095 ( 3) covalent geometry : bond 0.00334 (20775) covalent geometry : angle 0.61207 (28148) *********************** 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 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: A 215 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6398 (tmt) REVERT: A 365 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8123 (ptp-110) REVERT: A 373 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 584 LYS cc_start: 0.8330 (pttm) cc_final: 0.7554 (pmmt) REVERT: A 1156 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6954 (pm20) REVERT: A 1167 SER cc_start: 0.9079 (m) cc_final: 0.8837 (m) REVERT: A 1205 MET cc_start: 0.5323 (mmt) cc_final: 0.5059 (mpp) REVERT: A 1429 GLN cc_start: 0.6276 (mp10) cc_final: 0.5701 (pp30) REVERT: A 1433 MET cc_start: 0.4341 (ppp) cc_final: 0.2115 (mmm) REVERT: A 1472 TRP cc_start: 0.7533 (t60) cc_final: 0.6780 (t-100) REVERT: A 1504 CYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5727 (m) REVERT: A 1793 MET cc_start: 0.6148 (ppp) cc_final: 0.5760 (ppp) REVERT: A 1836 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6473 (mt0) REVERT: B 357 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7742 (mmtm) REVERT: B 367 LEU cc_start: 0.7253 (tm) cc_final: 0.6983 (mt) REVERT: B 389 LEU cc_start: 0.6158 (mt) cc_final: 0.5913 (tt) REVERT: B 391 GLU cc_start: 0.7525 (pt0) cc_final: 0.7279 (pt0) REVERT: B 405 LEU cc_start: 0.5853 (mm) cc_final: 0.5378 (pp) REVERT: D 64 TYR cc_start: 0.8045 (m-80) cc_final: 0.7057 (m-80) REVERT: D 197 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6890 (tmm-80) REVERT: D 366 GLU cc_start: 0.7127 (tt0) cc_final: 0.6866 (mm-30) REVERT: D 526 ASN cc_start: 0.8994 (t0) cc_final: 0.8657 (t0) REVERT: D 589 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7758 (mtp85) REVERT: D 653 PHE cc_start: 0.6775 (m-80) cc_final: 0.6154 (m-80) REVERT: D 744 TYR cc_start: 0.7437 (t80) cc_final: 0.7208 (t80) REVERT: D 772 ASN cc_start: 0.7166 (p0) cc_final: 0.6853 (p0) REVERT: D 848 MET cc_start: 0.1714 (mmp) cc_final: 0.1431 (tpt) REVERT: D 861 MET cc_start: 0.6498 (pmm) cc_final: 0.6269 (pmm) REVERT: D 870 GLN cc_start: 0.7596 (pt0) cc_final: 0.7247 (pp30) REVERT: D 1017 MET cc_start: 0.5372 (pmm) cc_final: 0.5035 (pmm) outliers start: 52 outliers final: 28 residues processed: 284 average time/residue: 1.0547 time to fit residues: 349.2183 Evaluate side-chains 278 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1589 GLN B 363 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** 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 = 0.4157 r_free = 0.4157 target = 0.182000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120246 restraints weight = 27043.741| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.21 r_work: 0.3296 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20803 Z= 0.129 Angle : 0.611 13.224 28221 Z= 0.305 Chirality : 0.044 0.218 3199 Planarity : 0.004 0.080 3479 Dihedral : 8.972 101.272 3808 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 2.19 % Allowed : 19.56 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.18), residues: 2414 helix: 0.81 (0.15), residues: 1207 sheet: -1.54 (0.33), residues: 220 loop : -1.32 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 PHE 0.032 0.001 PHE D 780 TYR 0.024 0.001 TYR D 426 ARG 0.006 0.000 ARG B 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 11) link_NAG-ASN : angle 3.19959 ( 33) link_BETA1-4 : bond 0.00600 ( 5) link_BETA1-4 : angle 1.87256 ( 15) hydrogen bonds : bond 0.03319 ( 923) hydrogen bonds : angle 4.30266 ( 2622) SS BOND : bond 0.00148 ( 11) SS BOND : angle 1.12698 ( 22) link_BETA1-3 : bond 0.00859 ( 1) link_BETA1-3 : angle 3.60735 ( 3) covalent geometry : bond 0.00305 (20775) covalent geometry : angle 0.59786 (28148) *********************** 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 299 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 215 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6406 (tmt) REVERT: A 365 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8128 (ptp-110) REVERT: A 373 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 522 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: A 530 MET cc_start: 0.7240 (tmm) cc_final: 0.6754 (tmt) REVERT: A 1156 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6916 (pm20) REVERT: A 1167 SER cc_start: 0.9103 (m) cc_final: 0.8886 (m) REVERT: A 1205 MET cc_start: 0.5290 (mmt) cc_final: 0.5042 (mpp) REVERT: A 1429 GLN cc_start: 0.6341 (mp10) cc_final: 0.5791 (pp30) REVERT: A 1472 TRP cc_start: 0.7542 (t60) cc_final: 0.6840 (t-100) REVERT: A 1504 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5751 (m) REVERT: A 1793 MET cc_start: 0.6087 (ppp) cc_final: 0.5682 (ppp) REVERT: A 1836 GLN cc_start: 0.7194 (tp-100) cc_final: 0.6473 (mt0) REVERT: B 357 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7738 (mmtm) REVERT: B 367 LEU cc_start: 0.7230 (tm) cc_final: 0.6982 (mt) REVERT: B 383 GLU cc_start: 0.4777 (pm20) cc_final: 0.4415 (pp20) REVERT: B 389 LEU cc_start: 0.6117 (mt) cc_final: 0.5889 (tt) REVERT: B 405 LEU cc_start: 0.5995 (mm) cc_final: 0.5503 (pp) REVERT: D 64 TYR cc_start: 0.8053 (m-80) cc_final: 0.7083 (m-80) REVERT: D 197 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6882 (tmm-80) REVERT: D 366 GLU cc_start: 0.7071 (tt0) cc_final: 0.6839 (mm-30) REVERT: D 482 GLN cc_start: 0.8281 (mt0) cc_final: 0.7790 (mp10) REVERT: D 526 ASN cc_start: 0.8996 (t0) cc_final: 0.8663 (t0) REVERT: D 589 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7703 (mtp85) REVERT: D 653 PHE cc_start: 0.6812 (m-80) cc_final: 0.6212 (m-80) REVERT: D 744 TYR cc_start: 0.7449 (t80) cc_final: 0.7226 (t80) REVERT: D 772 ASN cc_start: 0.7216 (p0) cc_final: 0.6878 (p0) REVERT: D 848 MET cc_start: 0.1587 (mmp) cc_final: 0.1317 (tpt) REVERT: D 861 MET cc_start: 0.6284 (pmm) cc_final: 0.6054 (pmm) REVERT: D 870 GLN cc_start: 0.7572 (pt0) cc_final: 0.7174 (pp30) REVERT: D 1017 MET cc_start: 0.5347 (OUTLIER) cc_final: 0.5009 (pmm) outliers start: 47 outliers final: 28 residues processed: 282 average time/residue: 1.0515 time to fit residues: 346.1021 Evaluate side-chains 279 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1017 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 121 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1589 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.181958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122469 restraints weight = 26922.584| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.51 r_work: 0.3290 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 20803 Z= 0.131 Angle : 0.620 13.169 28221 Z= 0.308 Chirality : 0.044 0.285 3199 Planarity : 0.004 0.081 3479 Dihedral : 8.909 101.460 3808 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.24 % Allowed : 20.21 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.18), residues: 2414 helix: 0.87 (0.15), residues: 1204 sheet: -1.52 (0.33), residues: 226 loop : -1.35 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.006 0.001 HIS A1760 PHE 0.029 0.001 PHE A1480 TYR 0.016 0.001 TYR A1765 ARG 0.007 0.000 ARG A1789 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 11) link_NAG-ASN : angle 3.16648 ( 33) link_BETA1-4 : bond 0.00569 ( 5) link_BETA1-4 : angle 1.81539 ( 15) hydrogen bonds : bond 0.03332 ( 923) hydrogen bonds : angle 4.27592 ( 2622) SS BOND : bond 0.00151 ( 11) SS BOND : angle 1.10317 ( 22) link_BETA1-3 : bond 0.00846 ( 1) link_BETA1-3 : angle 3.54177 ( 3) covalent geometry : bond 0.00317 (20775) covalent geometry : angle 0.60748 (28148) *********************** 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 293 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 138 GLU cc_start: 0.7326 (tp30) cc_final: 0.6588 (tt0) REVERT: A 215 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6405 (tmt) REVERT: A 365 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8125 (ptp-110) REVERT: A 373 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 522 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: A 530 MET cc_start: 0.7369 (tmm) cc_final: 0.7130 (tmt) REVERT: A 1156 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6916 (pm20) REVERT: A 1167 SER cc_start: 0.9088 (m) cc_final: 0.8866 (m) REVERT: A 1205 MET cc_start: 0.5289 (mmt) cc_final: 0.5039 (mpp) REVERT: A 1429 GLN cc_start: 0.6371 (mp10) cc_final: 0.5828 (pp30) REVERT: A 1433 MET cc_start: 0.4144 (ppp) cc_final: 0.2120 (mmm) REVERT: A 1472 TRP cc_start: 0.7542 (t60) cc_final: 0.6865 (t-100) REVERT: A 1504 CYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5689 (m) REVERT: A 1793 MET cc_start: 0.6060 (ppp) cc_final: 0.5666 (ppp) REVERT: A 1836 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6407 (mt0) REVERT: B 357 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7785 (mmtm) REVERT: B 367 LEU cc_start: 0.7234 (tm) cc_final: 0.7019 (mt) REVERT: B 383 GLU cc_start: 0.4795 (pm20) cc_final: 0.4454 (pp20) REVERT: B 389 LEU cc_start: 0.6060 (mt) cc_final: 0.5834 (tt) REVERT: B 405 LEU cc_start: 0.5994 (mm) cc_final: 0.5572 (pp) REVERT: D 64 TYR cc_start: 0.8071 (m-80) cc_final: 0.7160 (m-80) REVERT: D 197 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6885 (tmm-80) REVERT: D 366 GLU cc_start: 0.7094 (tt0) cc_final: 0.6869 (mm-30) REVERT: D 482 GLN cc_start: 0.8294 (mt0) cc_final: 0.7792 (mp10) REVERT: D 526 ASN cc_start: 0.9005 (t0) cc_final: 0.8675 (t0) REVERT: D 589 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7705 (mtp85) REVERT: D 653 PHE cc_start: 0.6757 (m-80) cc_final: 0.6140 (m-80) REVERT: D 735 VAL cc_start: 0.8132 (t) cc_final: 0.7884 (p) REVERT: D 744 TYR cc_start: 0.7464 (t80) cc_final: 0.7243 (t80) REVERT: D 772 ASN cc_start: 0.7123 (p0) cc_final: 0.6811 (p0) REVERT: D 793 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7221 (ttm) REVERT: D 848 MET cc_start: 0.1619 (mmp) cc_final: 0.1302 (tpt) REVERT: D 861 MET cc_start: 0.6327 (pmm) cc_final: 0.5868 (pmm) REVERT: D 870 GLN cc_start: 0.7538 (pt0) cc_final: 0.7227 (pp30) REVERT: D 1017 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.5078 (pmm) outliers start: 48 outliers final: 29 residues processed: 274 average time/residue: 1.0621 time to fit residues: 341.9832 Evaluate side-chains 278 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1017 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 171 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1589 GLN A1602 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** 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 = 0.4149 r_free = 0.4149 target = 0.181204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122302 restraints weight = 26996.564| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.57 r_work: 0.3274 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 20803 Z= 0.149 Angle : 0.642 14.746 28221 Z= 0.319 Chirality : 0.045 0.281 3199 Planarity : 0.004 0.080 3479 Dihedral : 8.944 102.036 3808 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 1.96 % Allowed : 20.59 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.18), residues: 2414 helix: 0.82 (0.15), residues: 1211 sheet: -1.44 (0.33), residues: 240 loop : -1.32 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.006 0.001 HIS A1760 PHE 0.029 0.001 PHE A1480 TYR 0.023 0.001 TYR D1068 ARG 0.010 0.000 ARG B 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 11) link_NAG-ASN : angle 3.16306 ( 33) link_BETA1-4 : bond 0.00593 ( 5) link_BETA1-4 : angle 1.80044 ( 15) hydrogen bonds : bond 0.03439 ( 923) hydrogen bonds : angle 4.31976 ( 2622) SS BOND : bond 0.00162 ( 11) SS BOND : angle 1.15063 ( 22) link_BETA1-3 : bond 0.00914 ( 1) link_BETA1-3 : angle 3.47018 ( 3) covalent geometry : bond 0.00359 (20775) covalent geometry : angle 0.63033 (28148) ********************** 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 284 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 215 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6424 (tmt) REVERT: A 365 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8069 (ptp-110) REVERT: A 373 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 518 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7332 (tt) REVERT: A 522 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: A 530 MET cc_start: 0.7292 (tmm) cc_final: 0.7055 (tmt) REVERT: A 1156 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6977 (pm20) REVERT: A 1167 SER cc_start: 0.9053 (m) cc_final: 0.8779 (m) REVERT: A 1205 MET cc_start: 0.5322 (mmt) cc_final: 0.5044 (mpp) REVERT: A 1429 GLN cc_start: 0.6365 (mp10) cc_final: 0.5754 (pp30) REVERT: A 1433 MET cc_start: 0.4179 (ppp) cc_final: 0.2054 (mmm) REVERT: A 1472 TRP cc_start: 0.7565 (t60) cc_final: 0.6942 (t-100) REVERT: A 1504 CYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5778 (m) REVERT: A 1793 MET cc_start: 0.6130 (ppp) cc_final: 0.5739 (ppp) REVERT: A 1836 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6401 (mt0) REVERT: A 1857 MET cc_start: 0.4865 (ttp) cc_final: 0.4603 (ttp) REVERT: B 248 MET cc_start: 0.7409 (mmp) cc_final: 0.6850 (mmm) REVERT: B 357 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7758 (mmtm) REVERT: B 367 LEU cc_start: 0.7189 (tm) cc_final: 0.6985 (mt) REVERT: B 383 GLU cc_start: 0.4731 (pm20) cc_final: 0.4376 (pp20) REVERT: B 389 LEU cc_start: 0.6002 (mt) cc_final: 0.5764 (tt) REVERT: B 391 GLU cc_start: 0.7134 (pt0) cc_final: 0.5911 (pp20) REVERT: B 405 LEU cc_start: 0.6023 (mm) cc_final: 0.5590 (pp) REVERT: D 64 TYR cc_start: 0.8025 (m-80) cc_final: 0.7094 (m-80) REVERT: D 197 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6907 (tmm-80) REVERT: D 366 GLU cc_start: 0.7106 (tt0) cc_final: 0.6889 (mm-30) REVERT: D 482 GLN cc_start: 0.8295 (mt0) cc_final: 0.7778 (mp10) REVERT: D 526 ASN cc_start: 0.9014 (t0) cc_final: 0.8677 (t0) REVERT: D 589 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7671 (mtp85) REVERT: D 653 PHE cc_start: 0.6747 (m-80) cc_final: 0.6087 (m-80) REVERT: D 744 TYR cc_start: 0.7481 (t80) cc_final: 0.7241 (t80) REVERT: D 772 ASN cc_start: 0.7033 (p0) cc_final: 0.6725 (p0) REVERT: D 793 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7238 (ttm) REVERT: D 848 MET cc_start: 0.1739 (mmp) cc_final: 0.1386 (tpt) REVERT: D 861 MET cc_start: 0.6225 (pmm) cc_final: 0.5911 (pmm) REVERT: D 870 GLN cc_start: 0.7513 (pt0) cc_final: 0.7140 (pp30) REVERT: D 1017 MET cc_start: 0.5374 (pmm) cc_final: 0.5002 (pmm) outliers start: 42 outliers final: 30 residues processed: 270 average time/residue: 1.0259 time to fit residues: 324.3623 Evaluate side-chains 277 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 134 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 145 optimal weight: 0.2980 chunk 201 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.2230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN A 727 HIS A1589 GLN D 481 ASN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.184526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122985 restraints weight = 27181.342| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.31 r_work: 0.3342 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 20803 Z= 0.108 Angle : 0.606 13.180 28221 Z= 0.302 Chirality : 0.043 0.231 3199 Planarity : 0.004 0.079 3479 Dihedral : 8.733 102.002 3808 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.33 % Rotamer: Outliers : 1.77 % Allowed : 20.87 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.28 (0.18), residues: 2414 helix: 1.00 (0.16), residues: 1202 sheet: -1.53 (0.34), residues: 218 loop : -1.31 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 185 HIS 0.006 0.001 HIS A1760 PHE 0.027 0.001 PHE A1480 TYR 0.016 0.001 TYR A1765 ARG 0.009 0.000 ARG B 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 3.11442 ( 33) link_BETA1-4 : bond 0.00613 ( 5) link_BETA1-4 : angle 1.71050 ( 15) hydrogen bonds : bond 0.03107 ( 923) hydrogen bonds : angle 4.20474 ( 2622) SS BOND : bond 0.00115 ( 11) SS BOND : angle 0.87393 ( 22) link_BETA1-3 : bond 0.00774 ( 1) link_BETA1-3 : angle 3.39218 ( 3) covalent geometry : bond 0.00244 (20775) covalent geometry : angle 0.59488 (28148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16599.72 seconds wall clock time: 285 minutes 30.23 seconds (17130.23 seconds total)