Starting phenix.real_space_refine on Sun Aug 24 16:45:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg5_33808/08_2025/7yg5_33808_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg5_33808/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yg5_33808/08_2025/7yg5_33808_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg5_33808/08_2025/7yg5_33808_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg5_33808/08_2025/7yg5_33808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg5_33808/08_2025/7yg5_33808.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.093 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.32, per 1000 atoms: 0.26 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: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.16 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: 4.77 Time building geometry restraints manager: 2.99 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: 2.920 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.680 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.180 ------------------------------------------------------------------------------- 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 : 16.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.015 0.001 ARG A 668 TYR 0.029 0.003 TYR D1068 PHE 0.035 0.003 PHE A1303 TRP 0.024 0.003 TRP A 88 HIS 0.010 0.002 HIS D 864 Details of bonding type rmsd covalent geometry : bond 0.01500 (20775) covalent geometry : angle 1.08894 (28148) SS BOND : bond 0.00424 ( 11) SS BOND : angle 3.67571 ( 22) hydrogen bonds : bond 0.15709 ( 923) hydrogen bonds : angle 7.29509 ( 2622) link_BETA1-3 : bond 0.00539 ( 1) link_BETA1-3 : angle 5.52302 ( 3) link_BETA1-4 : bond 0.00604 ( 5) link_BETA1-4 : angle 2.48427 ( 15) link_NAG-ASN : bond 0.00727 ( 11) link_NAG-ASN : angle 3.74064 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 0.889 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: 0.5584 time to fit residues: 184.6173 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 : 0.743 ------------------------------------------------------------------------------- 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 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 727 HIS A1288 ASN A1291 ASN A1429 GLN ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 864 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116644 restraints weight = 27080.581| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.57 r_work: 0.3186 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20803 Z= 0.244 Angle : 0.780 13.599 28221 Z= 0.394 Chirality : 0.049 0.296 3199 Planarity : 0.005 0.083 3479 Dihedral : 13.084 104.742 3822 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 1.91 % Allowed : 10.55 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.17), residues: 2414 helix: -0.62 (0.15), residues: 1193 sheet: -1.56 (0.33), residues: 235 loop : -1.96 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1182 TYR 0.031 0.002 TYR D 426 PHE 0.024 0.002 PHE A1449 TRP 0.018 0.002 TRP D 185 HIS 0.006 0.001 HIS D 864 Details of bonding type rmsd covalent geometry : bond 0.00581 (20775) covalent geometry : angle 0.76366 (28148) SS BOND : bond 0.00371 ( 11) SS BOND : angle 2.57620 ( 22) hydrogen bonds : bond 0.04751 ( 923) hydrogen bonds : angle 5.27781 ( 2622) link_BETA1-3 : bond 0.00755 ( 1) link_BETA1-3 : angle 5.07589 ( 3) link_BETA1-4 : bond 0.00659 ( 5) link_BETA1-4 : angle 2.51620 ( 15) link_NAG-ASN : bond 0.00495 ( 11) link_NAG-ASN : angle 3.67423 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8821 (tp30) cc_final: 0.8187 (tp30) REVERT: A 128 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 163 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8228 (ttt) REVERT: A 164 ASP cc_start: 0.7875 (t0) cc_final: 0.7637 (t0) REVERT: A 373 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 719 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 1157 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7420 (tmt) REVERT: A 1167 SER cc_start: 0.9154 (m) cc_final: 0.8927 (m) REVERT: A 1434 MET cc_start: 0.4109 (ttp) cc_final: 0.3767 (ttp) REVERT: A 1467 PHE cc_start: 0.6753 (p90) cc_final: 0.5900 (p90) REVERT: A 1591 TYR cc_start: 0.8076 (t80) cc_final: 0.7535 (t80) REVERT: A 1793 MET cc_start: 0.6273 (ppp) cc_final: 0.5731 (ppp) REVERT: A 1810 MET cc_start: 0.7687 (mmt) cc_final: 0.7467 (mpp) REVERT: B 247 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: B 353 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7428 (mp-120) REVERT: B 354 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7502 (mtt180) REVERT: D 64 TYR cc_start: 0.8076 (m-80) cc_final: 0.7013 (m-80) REVERT: D 108 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: D 366 GLU cc_start: 0.7206 (tt0) cc_final: 0.6770 (tm-30) REVERT: D 428 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 526 ASN cc_start: 0.9001 (t0) cc_final: 0.8772 (t0) REVERT: D 599 TYR cc_start: 0.8331 (m-10) cc_final: 0.8057 (m-10) REVERT: D 653 PHE cc_start: 0.6993 (m-80) cc_final: 0.6075 (m-10) REVERT: D 744 TYR cc_start: 0.7344 (t80) cc_final: 0.7072 (t80) REVERT: D 772 ASN cc_start: 0.7302 (p0) cc_final: 0.6976 (p0) REVERT: D 848 MET cc_start: 0.1803 (mmp) cc_final: 0.1440 (mmt) REVERT: D 892 TYR cc_start: 0.8387 (m-10) cc_final: 0.8110 (m-10) REVERT: D 977 GLU cc_start: 0.8169 (tp30) cc_final: 0.7686 (tm-30) REVERT: D 1036 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (tt0) outliers start: 41 outliers final: 11 residues processed: 270 average time/residue: 0.5482 time to fit residues: 170.9418 Evaluate side-chains 247 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 689 PHE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 1157 MET 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 247 MET Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 1036 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 31 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1357 ASN 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** D 717 GLN D 864 HIS D 870 GLN ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 985 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117739 restraints weight = 27068.761| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.49 r_work: 0.3227 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 20803 Z= 0.186 Angle : 0.702 13.533 28221 Z= 0.351 Chirality : 0.046 0.262 3199 Planarity : 0.005 0.079 3479 Dihedral : 11.440 104.003 3812 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.12 % Favored : 91.80 % Rotamer: Outliers : 2.24 % Allowed : 13.82 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.17), residues: 2414 helix: -0.21 (0.15), residues: 1197 sheet: -1.75 (0.32), residues: 237 loop : -1.80 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 230 TYR 0.013 0.001 TYR D 68 PHE 0.022 0.002 PHE A1449 TRP 0.018 0.001 TRP D 185 HIS 0.009 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00444 (20775) covalent geometry : angle 0.68550 (28148) SS BOND : bond 0.00542 ( 11) SS BOND : angle 2.20336 ( 22) hydrogen bonds : bond 0.04181 ( 923) hydrogen bonds : angle 4.91643 ( 2622) link_BETA1-3 : bond 0.00872 ( 1) link_BETA1-3 : angle 4.92420 ( 3) link_BETA1-4 : bond 0.00704 ( 5) link_BETA1-4 : angle 2.46797 ( 15) link_NAG-ASN : bond 0.00500 ( 11) link_NAG-ASN : angle 3.50098 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8793 (tp30) cc_final: 0.8196 (tp30) REVERT: A 128 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 373 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 719 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 1167 SER cc_start: 0.9132 (m) cc_final: 0.8893 (m) REVERT: A 1205 MET cc_start: 0.5325 (mmt) cc_final: 0.5089 (mpp) REVERT: A 1434 MET cc_start: 0.3992 (ttp) cc_final: 0.3771 (ttp) REVERT: A 1591 TYR cc_start: 0.8033 (t80) cc_final: 0.7441 (t80) REVERT: A 1793 MET cc_start: 0.6204 (ppp) cc_final: 0.5750 (ppp) REVERT: A 1810 MET cc_start: 0.7885 (mmt) cc_final: 0.7639 (mpp) REVERT: B 354 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7275 (mtt180) REVERT: B 391 GLU cc_start: 0.7581 (pt0) cc_final: 0.7314 (pt0) REVERT: D 64 TYR cc_start: 0.8084 (m-80) cc_final: 0.7015 (m-80) REVERT: D 246 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8621 (tm-30) REVERT: D 287 ASP cc_start: 0.8550 (m-30) cc_final: 0.8219 (m-30) REVERT: D 366 GLU cc_start: 0.7307 (tt0) cc_final: 0.6868 (mm-30) REVERT: D 526 ASN cc_start: 0.9005 (t0) cc_final: 0.8724 (t0) REVERT: D 599 TYR cc_start: 0.8185 (m-10) cc_final: 0.7842 (m-10) REVERT: D 653 PHE cc_start: 0.6933 (m-80) cc_final: 0.6153 (m-80) REVERT: D 744 TYR cc_start: 0.7394 (t80) cc_final: 0.7081 (t80) REVERT: D 772 ASN cc_start: 0.7284 (p0) cc_final: 0.6954 (p0) REVERT: D 848 MET cc_start: 0.1640 (mmp) cc_final: 0.1305 (tpt) REVERT: D 870 GLN cc_start: 0.7526 (pt0) cc_final: 0.7104 (pp30) REVERT: D 892 TYR cc_start: 0.8304 (m-10) cc_final: 0.7904 (m-10) REVERT: D 977 GLU cc_start: 0.7963 (tp30) cc_final: 0.7616 (tm-30) REVERT: D 1036 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7410 (tt0) outliers start: 48 outliers final: 17 residues processed: 286 average time/residue: 0.4583 time to fit residues: 152.2257 Evaluate side-chains 252 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL 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 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 882 LEU Chi-restraints excluded: chain D residue 1036 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 10 optimal weight: 0.0050 chunk 105 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 165 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.4892 ------------------------------------------------------------------------------- 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 A1429 GLN A1589 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 554 GLN ** D 676 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 = 0.4146 r_free = 0.4146 target = 0.180896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120517 restraints weight = 27069.923| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.51 r_work: 0.3271 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 20803 Z= 0.123 Angle : 0.641 13.548 28221 Z= 0.321 Chirality : 0.044 0.236 3199 Planarity : 0.004 0.076 3479 Dihedral : 10.013 102.056 3808 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 2.38 % Allowed : 16.06 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.17), residues: 2414 helix: 0.30 (0.15), residues: 1184 sheet: -1.67 (0.33), residues: 234 loop : -1.54 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 230 TYR 0.030 0.001 TYR D 426 PHE 0.019 0.001 PHE D 780 TRP 0.018 0.001 TRP D 185 HIS 0.010 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00279 (20775) covalent geometry : angle 0.62340 (28148) SS BOND : bond 0.00436 ( 11) SS BOND : angle 2.28765 ( 22) hydrogen bonds : bond 0.03559 ( 923) hydrogen bonds : angle 4.59053 ( 2622) link_BETA1-3 : bond 0.00708 ( 1) link_BETA1-3 : angle 4.58307 ( 3) link_BETA1-4 : bond 0.00695 ( 5) link_BETA1-4 : angle 2.46604 ( 15) link_NAG-ASN : bond 0.00499 ( 11) link_NAG-ASN : angle 3.40746 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8637 (tp30) cc_final: 0.8085 (tp30) REVERT: A 128 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 138 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6578 (tt0) REVERT: A 215 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6359 (tmt) REVERT: A 373 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 530 MET cc_start: 0.7472 (tmm) cc_final: 0.7180 (tmt) REVERT: A 719 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 1157 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7226 (tmt) REVERT: A 1167 SER cc_start: 0.9105 (m) cc_final: 0.8881 (m) REVERT: A 1205 MET cc_start: 0.5338 (mmt) cc_final: 0.5082 (mpp) REVERT: A 1470 ARG cc_start: 0.7161 (tpt-90) cc_final: 0.6953 (mmm-85) REVERT: A 1472 TRP cc_start: 0.7523 (t60) cc_final: 0.7165 (t60) REVERT: A 1793 MET cc_start: 0.6209 (ppp) cc_final: 0.5760 (ppp) REVERT: A 1810 MET cc_start: 0.7900 (mmt) cc_final: 0.7644 (mpp) REVERT: B 367 LEU cc_start: 0.6971 (tm) cc_final: 0.6729 (mt) REVERT: B 391 GLU cc_start: 0.7539 (pt0) cc_final: 0.7313 (pt0) REVERT: B 405 LEU cc_start: 0.5643 (mm) cc_final: 0.5102 (pp) REVERT: D 64 TYR cc_start: 0.8138 (m-80) cc_final: 0.7089 (m-80) REVERT: D 197 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6895 (tmm-80) REVERT: D 287 ASP cc_start: 0.8451 (m-30) cc_final: 0.8127 (m-30) REVERT: D 366 GLU cc_start: 0.7217 (tt0) cc_final: 0.6746 (mm-30) REVERT: D 461 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8837 (p) REVERT: D 526 ASN cc_start: 0.9009 (t0) cc_final: 0.8689 (t0) REVERT: D 599 TYR cc_start: 0.8085 (m-10) cc_final: 0.7840 (m-10) REVERT: D 653 PHE cc_start: 0.6830 (m-80) cc_final: 0.6176 (m-80) REVERT: D 744 TYR cc_start: 0.7332 (t80) cc_final: 0.7036 (t80) REVERT: D 772 ASN cc_start: 0.7245 (p0) cc_final: 0.6920 (p0) REVERT: D 848 MET cc_start: 0.1682 (mmp) cc_final: 0.1254 (tpt) REVERT: D 870 GLN cc_start: 0.7505 (pt0) cc_final: 0.7155 (pp30) REVERT: D 977 GLU cc_start: 0.7716 (tp30) cc_final: 0.7372 (tm-30) outliers start: 51 outliers final: 24 residues processed: 295 average time/residue: 0.5066 time to fit residues: 173.8325 Evaluate side-chains 260 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 553 PHE 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 1257 LEU Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1467 PHE 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 197 ARG 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 481 ASN Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 150 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 0.0670 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.2722 ------------------------------------------------------------------------------- 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 A1725 ASN D 108 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114508 restraints weight = 26915.583| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.15 r_work: 0.3223 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 20803 Z= 0.245 Angle : 0.702 13.345 28221 Z= 0.351 Chirality : 0.048 0.251 3199 Planarity : 0.005 0.075 3479 Dihedral : 9.960 102.361 3808 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.71 % Favored : 92.25 % Rotamer: Outliers : 2.71 % Allowed : 17.65 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2414 helix: 0.15 (0.15), residues: 1196 sheet: -1.71 (0.33), residues: 224 loop : -1.67 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.021 0.002 TYR A 585 PHE 0.021 0.002 PHE D 775 TRP 0.014 0.002 TRP D 185 HIS 0.009 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00594 (20775) covalent geometry : angle 0.68680 (28148) SS BOND : bond 0.00270 ( 11) SS BOND : angle 2.04683 ( 22) hydrogen bonds : bond 0.04093 ( 923) hydrogen bonds : angle 4.69810 ( 2622) link_BETA1-3 : bond 0.00681 ( 1) link_BETA1-3 : angle 4.32288 ( 3) link_BETA1-4 : bond 0.00659 ( 5) link_BETA1-4 : angle 2.36092 ( 15) link_NAG-ASN : bond 0.00487 ( 11) link_NAG-ASN : angle 3.39259 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 472 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.4332 (tmt) REVERT: A 719 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 1157 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7412 (tmt) REVERT: A 1167 SER cc_start: 0.9128 (m) cc_final: 0.8912 (m) REVERT: A 1205 MET cc_start: 0.5312 (mmt) cc_final: 0.5020 (mpp) REVERT: A 1274 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: A 1429 GLN cc_start: 0.6856 (mp10) cc_final: 0.6317 (pp30) REVERT: A 1793 MET cc_start: 0.6246 (ppp) cc_final: 0.5797 (ppp) REVERT: A 1810 MET cc_start: 0.7751 (mmt) cc_final: 0.7530 (mpp) REVERT: A 1836 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6518 (mt0) REVERT: B 247 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7111 (mtt) REVERT: B 354 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7285 (mtt180) REVERT: B 357 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7744 (mppt) REVERT: B 367 LEU cc_start: 0.6891 (tm) cc_final: 0.6677 (mt) REVERT: B 391 GLU cc_start: 0.7594 (pt0) cc_final: 0.7316 (pt0) REVERT: D 64 TYR cc_start: 0.8071 (m-80) cc_final: 0.7055 (m-80) REVERT: D 197 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6933 (tmm-80) REVERT: D 366 GLU cc_start: 0.7146 (tt0) cc_final: 0.6782 (mm-30) REVERT: D 526 ASN cc_start: 0.9007 (t0) cc_final: 0.8696 (t0) REVERT: D 653 PHE cc_start: 0.6915 (m-80) cc_final: 0.6272 (m-80) REVERT: D 744 TYR cc_start: 0.7482 (t80) cc_final: 0.7216 (t80) REVERT: D 772 ASN cc_start: 0.7306 (p0) cc_final: 0.6991 (p0) REVERT: D 793 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7237 (ttm) REVERT: D 848 MET cc_start: 0.1696 (mmp) cc_final: 0.1323 (tpt) REVERT: D 870 GLN cc_start: 0.7513 (pt0) cc_final: 0.7107 (pp30) REVERT: D 977 GLU cc_start: 0.7783 (tp30) cc_final: 0.7522 (mm-30) outliers start: 58 outliers final: 32 residues processed: 291 average time/residue: 0.4952 time to fit residues: 167.6950 Evaluate side-chains 279 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 472 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 633 ASP 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 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 1274 LYS Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1484 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 247 MET 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 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 461 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 979 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 980 GLN ** 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 = 0.4137 r_free = 0.4137 target = 0.180031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121148 restraints weight = 26839.380| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.50 r_work: 0.3259 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 20803 Z= 0.136 Angle : 0.639 13.498 28221 Z= 0.319 Chirality : 0.045 0.230 3199 Planarity : 0.004 0.077 3479 Dihedral : 9.617 101.931 3808 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.71 % Allowed : 18.21 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.17), residues: 2414 helix: 0.47 (0.15), residues: 1189 sheet: -1.66 (0.33), residues: 240 loop : -1.54 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 230 TYR 0.032 0.001 TYR D 426 PHE 0.030 0.001 PHE A1480 TRP 0.017 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00322 (20775) covalent geometry : angle 0.62504 (28148) SS BOND : bond 0.00186 ( 11) SS BOND : angle 1.43735 ( 22) hydrogen bonds : bond 0.03545 ( 923) hydrogen bonds : angle 4.49415 ( 2622) link_BETA1-3 : bond 0.00840 ( 1) link_BETA1-3 : angle 3.98231 ( 3) link_BETA1-4 : bond 0.00621 ( 5) link_BETA1-4 : angle 2.15877 ( 15) link_NAG-ASN : bond 0.00494 ( 11) link_NAG-ASN : angle 3.32694 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.520 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: 0.8096 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: A 365 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8118 (ptp-110) REVERT: A 373 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 472 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.4191 (tmt) REVERT: A 518 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (tt) REVERT: A 522 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5861 (mp0) REVERT: A 719 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 1157 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (tmt) REVERT: A 1167 SER cc_start: 0.9122 (m) cc_final: 0.8914 (m) REVERT: A 1205 MET cc_start: 0.5260 (mmt) cc_final: 0.4960 (mpp) REVERT: A 1429 GLN cc_start: 0.6920 (mp10) cc_final: 0.6384 (pp30) REVERT: A 1504 CYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5682 (m) REVERT: A 1793 MET cc_start: 0.6253 (ppp) cc_final: 0.5814 (ppp) REVERT: A 1836 GLN cc_start: 0.7239 (tp-100) cc_final: 0.6529 (mt0) REVERT: B 247 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7001 (mtt) REVERT: B 354 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7209 (mtt180) REVERT: B 389 LEU cc_start: 0.6135 (mt) cc_final: 0.5847 (tt) REVERT: B 391 GLU cc_start: 0.7469 (pt0) cc_final: 0.7087 (pt0) REVERT: D 64 TYR cc_start: 0.8064 (m-80) cc_final: 0.7082 (m-80) REVERT: D 366 GLU cc_start: 0.7209 (tt0) cc_final: 0.6860 (mm-30) REVERT: D 526 ASN cc_start: 0.9022 (t0) cc_final: 0.8696 (t0) REVERT: D 589 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7895 (mtp85) REVERT: D 653 PHE cc_start: 0.6877 (m-80) cc_final: 0.6232 (m-80) REVERT: D 744 TYR cc_start: 0.7432 (t80) cc_final: 0.7176 (t80) REVERT: D 772 ASN cc_start: 0.7275 (p0) cc_final: 0.6960 (p0) REVERT: D 801 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: D 848 MET cc_start: 0.1592 (mmp) cc_final: 0.1252 (tpt) REVERT: D 870 GLN cc_start: 0.7492 (pt0) cc_final: 0.7088 (pp30) REVERT: D 977 GLU cc_start: 0.7678 (tp30) cc_final: 0.7475 (mm-30) REVERT: D 1036 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7172 (tt0) outliers start: 58 outliers final: 27 residues processed: 289 average time/residue: 0.4691 time to fit residues: 157.9834 Evaluate side-chains 271 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 472 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 564 THR 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 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 1384 VAL 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 247 MET 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 393 ASN Chi-restraints excluded: chain D residue 461 THR 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 801 TYR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1036 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 106 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.2980 chunk 200 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A1291 ASN A1589 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.181150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122506 restraints weight = 27047.401| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.43 r_work: 0.3293 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 20803 Z= 0.125 Angle : 0.629 13.346 28221 Z= 0.314 Chirality : 0.044 0.216 3199 Planarity : 0.004 0.078 3479 Dihedral : 9.308 101.177 3808 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.71 % Allowed : 19.14 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.18), residues: 2414 helix: 0.70 (0.15), residues: 1184 sheet: -1.61 (0.33), residues: 236 loop : -1.42 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 766 TYR 0.016 0.001 TYR A1765 PHE 0.030 0.001 PHE A1480 TRP 0.016 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00297 (20775) covalent geometry : angle 0.61591 (28148) SS BOND : bond 0.00150 ( 11) SS BOND : angle 1.23729 ( 22) hydrogen bonds : bond 0.03386 ( 923) hydrogen bonds : angle 4.38681 ( 2622) link_BETA1-3 : bond 0.00848 ( 1) link_BETA1-3 : angle 3.81934 ( 3) link_BETA1-4 : bond 0.00622 ( 5) link_BETA1-4 : angle 2.02786 ( 15) link_NAG-ASN : bond 0.00511 ( 11) link_NAG-ASN : angle 3.25091 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 215 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6383 (tmt) REVERT: A 365 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8179 (ptp-110) REVERT: A 373 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 518 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7306 (tt) REVERT: A 719 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 1156 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7033 (pm20) REVERT: A 1167 SER cc_start: 0.9110 (m) cc_final: 0.8904 (m) REVERT: A 1205 MET cc_start: 0.5307 (mmt) cc_final: 0.5001 (mpp) REVERT: A 1429 GLN cc_start: 0.6922 (mp10) cc_final: 0.6362 (pp30) REVERT: A 1472 TRP cc_start: 0.7587 (t60) cc_final: 0.6804 (t-100) REVERT: A 1504 CYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5693 (m) REVERT: A 1793 MET cc_start: 0.6211 (ppp) cc_final: 0.5783 (ppp) REVERT: A 1836 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6477 (mt0) REVERT: B 354 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7129 (mtt180) REVERT: B 367 LEU cc_start: 0.7221 (tm) cc_final: 0.6931 (mt) REVERT: B 389 LEU cc_start: 0.6102 (mt) cc_final: 0.5828 (tt) REVERT: B 391 GLU cc_start: 0.7428 (pt0) cc_final: 0.6854 (pt0) REVERT: B 405 LEU cc_start: 0.5785 (mm) cc_final: 0.5276 (pp) REVERT: D 64 TYR cc_start: 0.8002 (m-80) cc_final: 0.7035 (m-80) REVERT: D 366 GLU cc_start: 0.7157 (tt0) cc_final: 0.6838 (mm-30) REVERT: D 526 ASN cc_start: 0.8999 (t0) cc_final: 0.8662 (t0) REVERT: D 589 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7834 (mtp85) REVERT: D 653 PHE cc_start: 0.6836 (m-80) cc_final: 0.6240 (m-80) REVERT: D 678 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8662 (tm-30) REVERT: D 744 TYR cc_start: 0.7460 (t80) cc_final: 0.7234 (t80) REVERT: D 848 MET cc_start: 0.1413 (mmp) cc_final: 0.1128 (tpt) REVERT: D 870 GLN cc_start: 0.7599 (pt0) cc_final: 0.7233 (pp30) outliers start: 58 outliers final: 27 residues processed: 306 average time/residue: 0.4637 time to fit residues: 165.6895 Evaluate side-chains 278 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 349 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 633 ASP 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 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 A residue 1678 CYS 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 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 241 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 980 GLN ** 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 = 0.4145 r_free = 0.4145 target = 0.180785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122574 restraints weight = 26978.236| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.56 r_work: 0.3263 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 20803 Z= 0.135 Angle : 0.637 13.305 28221 Z= 0.317 Chirality : 0.044 0.214 3199 Planarity : 0.004 0.079 3479 Dihedral : 9.213 101.173 3808 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 2.33 % Allowed : 20.68 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.18), residues: 2414 helix: 0.75 (0.15), residues: 1191 sheet: -1.65 (0.34), residues: 220 loop : -1.39 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 766 TYR 0.022 0.001 TYR D 426 PHE 0.029 0.001 PHE A1480 TRP 0.015 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00324 (20775) covalent geometry : angle 0.62481 (28148) SS BOND : bond 0.00163 ( 11) SS BOND : angle 1.21710 ( 22) hydrogen bonds : bond 0.03440 ( 923) hydrogen bonds : angle 4.37843 ( 2622) link_BETA1-3 : bond 0.00864 ( 1) link_BETA1-3 : angle 3.72470 ( 3) link_BETA1-4 : bond 0.00600 ( 5) link_BETA1-4 : angle 1.93611 ( 15) link_NAG-ASN : bond 0.00504 ( 11) link_NAG-ASN : angle 3.23484 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 365 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8208 (ptp-110) REVERT: A 373 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 518 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7365 (tt) REVERT: A 522 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: A 719 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 1156 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6924 (pm20) REVERT: A 1157 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7201 (tmm) REVERT: A 1167 SER cc_start: 0.9123 (m) cc_final: 0.8912 (m) REVERT: A 1205 MET cc_start: 0.5318 (mmt) cc_final: 0.5011 (mpp) REVERT: A 1429 GLN cc_start: 0.6998 (mp10) cc_final: 0.6360 (pp30) REVERT: A 1472 TRP cc_start: 0.7587 (t60) cc_final: 0.6839 (t-100) REVERT: A 1504 CYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5768 (m) REVERT: A 1789 ARG cc_start: 0.6015 (tpp-160) cc_final: 0.5415 (tpt-90) REVERT: A 1793 MET cc_start: 0.6194 (ppp) cc_final: 0.5726 (ppp) REVERT: A 1836 GLN cc_start: 0.7178 (tp-100) cc_final: 0.6422 (mt0) REVERT: B 354 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7022 (mtt180) REVERT: B 367 LEU cc_start: 0.7250 (tm) cc_final: 0.6936 (mt) REVERT: B 383 GLU cc_start: 0.4554 (pm20) cc_final: 0.4283 (pp20) REVERT: B 389 LEU cc_start: 0.6136 (mt) cc_final: 0.5895 (tt) REVERT: B 391 GLU cc_start: 0.7366 (pt0) cc_final: 0.6765 (pt0) REVERT: B 405 LEU cc_start: 0.5831 (mm) cc_final: 0.5310 (pp) REVERT: D 64 TYR cc_start: 0.8010 (m-80) cc_final: 0.7030 (m-80) REVERT: D 366 GLU cc_start: 0.7146 (tt0) cc_final: 0.6890 (mm-30) REVERT: D 526 ASN cc_start: 0.9013 (t0) cc_final: 0.8674 (t0) REVERT: D 589 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7763 (mtp85) REVERT: D 653 PHE cc_start: 0.6827 (m-80) cc_final: 0.6189 (m-80) REVERT: D 678 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8648 (tm-30) REVERT: D 744 TYR cc_start: 0.7481 (t80) cc_final: 0.7244 (t80) REVERT: D 772 ASN cc_start: 0.7261 (p0) cc_final: 0.6932 (p0) REVERT: D 848 MET cc_start: 0.1567 (mmp) cc_final: 0.1288 (tpt) REVERT: D 858 PHE cc_start: 0.7727 (m-80) cc_final: 0.7308 (m-80) REVERT: D 870 GLN cc_start: 0.7621 (pt0) cc_final: 0.7182 (pp30) outliers start: 50 outliers final: 31 residues processed: 285 average time/residue: 0.4404 time to fit residues: 146.6064 Evaluate side-chains 281 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 633 ASP 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 1384 VAL 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 A residue 1641 ASN Chi-restraints excluded: chain A residue 1678 CYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 137 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 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 286 ASN A 727 HIS A1491 ASN A1589 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** 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 = 0.4152 r_free = 0.4152 target = 0.181537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122734 restraints weight = 26848.600| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.46 r_work: 0.3285 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 20803 Z= 0.124 Angle : 0.628 13.303 28221 Z= 0.313 Chirality : 0.044 0.212 3199 Planarity : 0.004 0.079 3479 Dihedral : 9.076 101.283 3808 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.43 % Allowed : 21.06 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.18), residues: 2414 helix: 0.83 (0.15), residues: 1189 sheet: -1.65 (0.34), residues: 226 loop : -1.36 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 766 TYR 0.016 0.001 TYR A1765 PHE 0.029 0.001 PHE A1480 TRP 0.016 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00295 (20775) covalent geometry : angle 0.61548 (28148) SS BOND : bond 0.00147 ( 11) SS BOND : angle 1.10942 ( 22) hydrogen bonds : bond 0.03339 ( 923) hydrogen bonds : angle 4.35893 ( 2622) link_BETA1-3 : bond 0.00883 ( 1) link_BETA1-3 : angle 3.62558 ( 3) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 1.87220 ( 15) link_NAG-ASN : bond 0.00511 ( 11) link_NAG-ASN : angle 3.20196 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 365 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8196 (ptp-110) REVERT: A 373 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 522 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: A 530 MET cc_start: 0.7113 (tmt) cc_final: 0.6601 (tmt) REVERT: A 719 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 1156 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6934 (pm20) REVERT: A 1167 SER cc_start: 0.9046 (m) cc_final: 0.8805 (m) REVERT: A 1205 MET cc_start: 0.5309 (mmt) cc_final: 0.5035 (mpp) REVERT: A 1429 GLN cc_start: 0.7078 (mp10) cc_final: 0.6410 (pp30) REVERT: A 1433 MET cc_start: 0.4017 (ppp) cc_final: 0.1964 (mmm) REVERT: A 1472 TRP cc_start: 0.7578 (t60) cc_final: 0.6863 (t-100) REVERT: A 1504 CYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5750 (m) REVERT: A 1793 MET cc_start: 0.6145 (ppp) cc_final: 0.5786 (ppp) REVERT: A 1836 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6415 (mt0) REVERT: A 1857 MET cc_start: 0.4887 (ttp) cc_final: 0.4617 (ttp) REVERT: B 354 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7132 (mtt180) REVERT: B 367 LEU cc_start: 0.7254 (tm) cc_final: 0.6979 (mt) REVERT: B 389 LEU cc_start: 0.6109 (mt) cc_final: 0.5883 (tt) REVERT: B 391 GLU cc_start: 0.7326 (pt0) cc_final: 0.6707 (pt0) REVERT: B 405 LEU cc_start: 0.6032 (mm) cc_final: 0.5583 (pp) REVERT: D 64 TYR cc_start: 0.8004 (m-80) cc_final: 0.7033 (m-80) REVERT: D 191 GLU cc_start: 0.8075 (pp20) cc_final: 0.7774 (pp20) REVERT: D 366 GLU cc_start: 0.7118 (tt0) cc_final: 0.6831 (mm-30) REVERT: D 526 ASN cc_start: 0.9002 (t0) cc_final: 0.8657 (t0) REVERT: D 589 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7728 (mtp85) REVERT: D 653 PHE cc_start: 0.6807 (m-80) cc_final: 0.6172 (m-80) REVERT: D 678 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 744 TYR cc_start: 0.7487 (t80) cc_final: 0.7244 (t80) REVERT: D 848 MET cc_start: 0.1491 (mmp) cc_final: 0.1249 (tpt) REVERT: D 870 GLN cc_start: 0.7526 (pt0) cc_final: 0.7210 (pp30) REVERT: D 1032 ILE cc_start: 0.8063 (mt) cc_final: 0.7837 (mp) outliers start: 52 outliers final: 32 residues processed: 290 average time/residue: 0.4857 time to fit residues: 164.7943 Evaluate side-chains 282 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 564 THR 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 1257 LEU Chi-restraints excluded: chain A residue 1384 VAL 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 A residue 1641 ASN Chi-restraints excluded: chain A residue 1678 CYS 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 207 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 54 optimal weight: 0.4980 chunk 218 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 194 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 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 ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122848 restraints weight = 26987.982| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.48 r_work: 0.3290 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 20803 Z= 0.124 Angle : 0.635 13.224 28221 Z= 0.315 Chirality : 0.044 0.209 3199 Planarity : 0.004 0.081 3479 Dihedral : 8.988 101.449 3808 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 1.77 % Allowed : 21.57 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2414 helix: 0.84 (0.15), residues: 1196 sheet: -1.65 (0.34), residues: 220 loop : -1.32 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 766 TYR 0.022 0.001 TYR D1068 PHE 0.030 0.001 PHE A1480 TRP 0.016 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00292 (20775) covalent geometry : angle 0.62309 (28148) SS BOND : bond 0.00148 ( 11) SS BOND : angle 1.07350 ( 22) hydrogen bonds : bond 0.03302 ( 923) hydrogen bonds : angle 4.33213 ( 2622) link_BETA1-3 : bond 0.00902 ( 1) link_BETA1-3 : angle 3.55480 ( 3) link_BETA1-4 : bond 0.00598 ( 5) link_BETA1-4 : angle 1.82818 ( 15) link_NAG-ASN : bond 0.00505 ( 11) link_NAG-ASN : angle 3.16851 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: A 365 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8164 (ptp-110) REVERT: A 373 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 530 MET cc_start: 0.7068 (tmt) cc_final: 0.6602 (tmt) REVERT: A 719 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 1156 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6956 (pm20) REVERT: A 1167 SER cc_start: 0.9045 (m) cc_final: 0.8810 (m) REVERT: A 1205 MET cc_start: 0.5368 (mmt) cc_final: 0.5115 (mpp) REVERT: A 1433 MET cc_start: 0.4034 (ppp) cc_final: 0.1988 (mmm) REVERT: A 1472 TRP cc_start: 0.7544 (t60) cc_final: 0.6859 (t-100) REVERT: A 1504 CYS cc_start: 0.6369 (OUTLIER) cc_final: 0.5916 (m) REVERT: A 1793 MET cc_start: 0.6149 (ppp) cc_final: 0.5793 (ppp) REVERT: A 1836 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6412 (mt0) REVERT: A 1857 MET cc_start: 0.4872 (ttp) cc_final: 0.4601 (ttp) REVERT: B 354 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7114 (mtt180) REVERT: B 367 LEU cc_start: 0.7279 (tm) cc_final: 0.6970 (mt) REVERT: B 383 GLU cc_start: 0.4536 (pm20) cc_final: 0.4316 (pp20) REVERT: B 389 LEU cc_start: 0.6142 (mt) cc_final: 0.5874 (tt) REVERT: B 391 GLU cc_start: 0.7260 (pt0) cc_final: 0.6616 (pt0) REVERT: B 405 LEU cc_start: 0.6060 (mm) cc_final: 0.5614 (pp) REVERT: D 64 TYR cc_start: 0.8054 (m-80) cc_final: 0.7092 (m-80) REVERT: D 366 GLU cc_start: 0.7071 (tt0) cc_final: 0.6855 (mm-30) REVERT: D 482 GLN cc_start: 0.8282 (mt0) cc_final: 0.7780 (mp10) REVERT: D 526 ASN cc_start: 0.9002 (t0) cc_final: 0.8660 (t0) REVERT: D 589 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7682 (mtp85) REVERT: D 653 PHE cc_start: 0.6821 (m-80) cc_final: 0.6193 (m-80) REVERT: D 678 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8673 (tm-30) REVERT: D 744 TYR cc_start: 0.7511 (t80) cc_final: 0.7272 (t80) REVERT: D 772 ASN cc_start: 0.7086 (p0) cc_final: 0.6874 (p0) REVERT: D 848 MET cc_start: 0.1535 (mmp) cc_final: 0.1324 (tpt) REVERT: D 870 GLN cc_start: 0.7437 (pt0) cc_final: 0.7173 (pp30) REVERT: D 1032 ILE cc_start: 0.8033 (mt) cc_final: 0.7828 (mp) outliers start: 38 outliers final: 32 residues processed: 284 average time/residue: 0.4704 time to fit residues: 156.3428 Evaluate side-chains 278 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 564 THR 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 1168 ILE Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1384 VAL 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 A residue 1641 ASN Chi-restraints excluded: chain A residue 1678 CYS 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 207 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 980 GLN ** 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 = 0.182014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121959 restraints weight = 26990.877| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.55 r_work: 0.3282 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20803 Z= 0.128 Angle : 0.644 14.498 28221 Z= 0.319 Chirality : 0.044 0.212 3199 Planarity : 0.004 0.078 3479 Dihedral : 8.935 101.772 3808 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 1.87 % Allowed : 21.85 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2414 helix: 0.87 (0.15), residues: 1197 sheet: -1.69 (0.34), residues: 220 loop : -1.32 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 766 TYR 0.015 0.001 TYR A1765 PHE 0.029 0.001 PHE A1480 TRP 0.016 0.001 TRP D 185 HIS 0.006 0.001 HIS A1760 Details of bonding type rmsd covalent geometry : bond 0.00305 (20775) covalent geometry : angle 0.63282 (28148) SS BOND : bond 0.00149 ( 11) SS BOND : angle 1.05437 ( 22) hydrogen bonds : bond 0.03301 ( 923) hydrogen bonds : angle 4.33232 ( 2622) link_BETA1-3 : bond 0.00784 ( 1) link_BETA1-3 : angle 3.54146 ( 3) link_BETA1-4 : bond 0.00599 ( 5) link_BETA1-4 : angle 1.80084 ( 15) link_NAG-ASN : bond 0.00515 ( 11) link_NAG-ASN : angle 3.15528 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7873.54 seconds wall clock time: 134 minutes 29.50 seconds (8069.50 seconds total)