Starting phenix.real_space_refine on Sat Jul 4 14:09:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg5_33808/07_2026/7yg5_33808_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg5_33808/07_2026/7yg5_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_33808/07_2026/7yg5_33808_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg5_33808/07_2026/7yg5_33808_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg5_33808/07_2026/7yg5_33808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg5_33808/07_2026/7yg5_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-dev-6108/lib/python3.11/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, 497 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'3PE': 2, 'R16': 6, 'TOR': 1, 'Y01': 9} Classifications: {'undetermined': 18} Link IDs: {None: 16} Chain breaks: 1 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, 112 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 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: 5.01, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 972.9 milliseconds 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 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: 0.69 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: 4.33 Time building geometry restraints manager: 2.50 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.330 Find NCS groups from input model: 0.080 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 are 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/Z covalent geometry : bond 0.01500 / 0.67 (20775) covalent geometry : angle 1.08894 / 0.61 (28148) SS BOND : bond 0.00424 / 0.26 ( 11) SS BOND : angle 3.67571 / 2.54 ( 22) hydrogen bonds : bond 0.15709 / 10.55 ( 923) hydrogen bonds : angle 7.29509 / 5.09 ( 2622) link_BETA1-3 : bond 0.00539 / 0.28 ( 1) link_BETA1-3 : angle 5.52302 / 3.40 ( 3) link_BETA1-4 : bond 0.00604 / 0.36 ( 5) link_BETA1-4 : angle 2.48427 / 1.74 ( 15) link_NAG-ASN : bond 0.00727 / 0.48 ( 11) link_NAG-ASN : angle 3.74064 / 2.33 ( 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 : 0.682 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: 0.5075 time to fit residues: 168.0184 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 : 0.602 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 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: 10.0000 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 294 ASN A 623 GLN A 727 HIS A1291 ASN A1429 GLN A1462 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 = 0.4097 r_free = 0.4097 target = 0.175968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116753 restraints weight = 27051.081| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.51 r_work: 0.3203 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 20803 Z= 0.229 Angle : 0.770 13.544 28221 Z= 0.389 Chirality : 0.048 0.289 3199 Planarity : 0.005 0.082 3479 Dihedral : 13.079 104.939 3822 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.41 % Favored : 91.47 % Rotamer: Outliers : 1.73 % Allowed : 10.13 % Favored : 88.14 % 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 are not related in a simple way. whole: -1.90 (0.17), residues: 2414 helix: -0.59 (0.15), residues: 1192 sheet: -1.53 (0.33), residues: 234 loop : -1.94 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1693 TYR 0.030 0.002 TYR D 426 PHE 0.023 0.002 PHE A1449 TRP 0.018 0.002 TRP D 185 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (20775) covalent geometry : angle 0.75340 / 0.39 (28148) SS BOND : bond 0.00495 / 0.35 ( 11) SS BOND : angle 2.65944 / 1.96 ( 22) hydrogen bonds : bond 0.04825 / 3.14 ( 923) hydrogen bonds : angle 5.28950 / 3.72 ( 2622) link_BETA1-3 : bond 0.00805 / 0.42 ( 1) link_BETA1-3 : angle 4.99089 / 3.28 ( 3) link_BETA1-4 : bond 0.00702 / 0.38 ( 5) link_BETA1-4 : angle 2.44793 / 1.66 ( 15) link_NAG-ASN : bond 0.00489 / 0.28 ( 11) link_NAG-ASN : angle 3.66206 / 2.28 ( 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 291 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8820 (tp30) cc_final: 0.8205 (tp30) REVERT: A 128 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 163 MET cc_start: 0.8493 (ppp) cc_final: 0.8233 (ttt) REVERT: A 164 ASP cc_start: 0.7907 (t0) cc_final: 0.7661 (t0) REVERT: A 373 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 719 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1157 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7416 (tmt) REVERT: A 1167 SER cc_start: 0.9166 (m) cc_final: 0.8939 (m) REVERT: A 1434 MET cc_start: 0.4135 (ttp) cc_final: 0.3795 (ttp) REVERT: A 1467 PHE cc_start: 0.6787 (p90) cc_final: 0.5941 (p90) REVERT: A 1591 TYR cc_start: 0.8059 (t80) cc_final: 0.7519 (t80) REVERT: A 1793 MET cc_start: 0.6280 (ppp) cc_final: 0.5739 (ppp) REVERT: A 1810 MET cc_start: 0.7700 (mmt) cc_final: 0.7457 (mpp) REVERT: B 249 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6952 (mm-40) REVERT: B 354 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7506 (mtt180) REVERT: D 64 TYR cc_start: 0.8082 (m-80) cc_final: 0.7021 (m-80) REVERT: D 108 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: D 366 GLU cc_start: 0.7205 (tt0) cc_final: 0.6739 (tm-30) REVERT: D 428 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 526 ASN cc_start: 0.8996 (t0) cc_final: 0.8776 (t0) REVERT: D 599 TYR cc_start: 0.8374 (m-10) cc_final: 0.8104 (m-10) REVERT: D 653 PHE cc_start: 0.6969 (m-80) cc_final: 0.6083 (m-10) REVERT: D 744 TYR cc_start: 0.7366 (t80) cc_final: 0.7116 (t80) REVERT: D 848 MET cc_start: 0.1899 (mmp) cc_final: 0.1536 (mmt) REVERT: D 892 TYR cc_start: 0.8393 (m-10) cc_final: 0.8163 (m-10) REVERT: D 977 GLU cc_start: 0.8171 (tp30) cc_final: 0.7664 (tm-30) outliers start: 37 outliers final: 10 residues processed: 270 average time/residue: 0.5313 time to fit residues: 166.4478 Evaluate side-chains 243 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU 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 1504 CYS Chi-restraints excluded: chain A residue 1541 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 31 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 HIS A1288 ASN ** A1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4116 r_free = 0.4116 target = 0.177974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118449 restraints weight = 27072.926| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.52 r_work: 0.3234 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 20803 Z= 0.169 Angle : 0.693 13.541 28221 Z= 0.347 Chirality : 0.046 0.260 3199 Planarity : 0.005 0.079 3479 Dihedral : 11.420 104.022 3812 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.04 % Favored : 91.92 % Rotamer: Outliers : 2.15 % Allowed : 13.49 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2414 helix: -0.17 (0.15), residues: 1197 sheet: -1.75 (0.32), residues: 237 loop : -1.72 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 230 TYR 0.014 0.001 TYR D 719 PHE 0.022 0.001 PHE A1449 TRP 0.017 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (20775) covalent geometry : angle 0.67667 / 0.34 (28148) SS BOND : bond 0.00312 / 0.21 ( 11) SS BOND : angle 2.15901 / 1.62 ( 22) hydrogen bonds : bond 0.04112 / 2.67 ( 923) hydrogen bonds : angle 4.88822 / 3.43 ( 2622) link_BETA1-3 : bond 0.00803 / 0.42 ( 1) link_BETA1-3 : angle 4.90760 / 3.16 ( 3) link_BETA1-4 : bond 0.00697 / 0.39 ( 5) link_BETA1-4 : angle 2.45664 / 1.69 ( 15) link_NAG-ASN : bond 0.00505 / 0.28 ( 11) link_NAG-ASN : angle 3.48814 / 2.14 ( 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: 46 poor density : 260 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8759 (tp30) cc_final: 0.8166 (tp30) REVERT: A 128 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 164 ASP cc_start: 0.7837 (t0) cc_final: 0.7631 (t0) REVERT: A 373 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 504 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8167 (tp) REVERT: A 719 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 1167 SER cc_start: 0.9122 (m) cc_final: 0.8884 (m) REVERT: A 1205 MET cc_start: 0.5291 (mmt) cc_final: 0.5051 (mpp) REVERT: A 1434 MET cc_start: 0.4057 (ttp) cc_final: 0.3838 (ttp) REVERT: A 1591 TYR cc_start: 0.8023 (t80) cc_final: 0.7495 (t80) REVERT: A 1793 MET cc_start: 0.6244 (ppp) cc_final: 0.5771 (ppp) REVERT: A 1810 MET cc_start: 0.7884 (mmt) cc_final: 0.7627 (mpp) REVERT: B 247 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: B 354 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7430 (mtt180) REVERT: D 64 TYR cc_start: 0.8083 (m-80) cc_final: 0.7017 (m-80) REVERT: D 246 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 366 GLU cc_start: 0.7282 (tt0) cc_final: 0.6831 (mm-30) REVERT: D 526 ASN cc_start: 0.9002 (t0) cc_final: 0.8720 (t0) REVERT: D 595 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 599 TYR cc_start: 0.8155 (m-10) cc_final: 0.7760 (m-10) REVERT: D 653 PHE cc_start: 0.6964 (m-80) cc_final: 0.6182 (m-80) REVERT: D 744 TYR cc_start: 0.7416 (t80) cc_final: 0.7118 (t80) REVERT: D 766 ARG cc_start: 0.8387 (ttt90) cc_final: 0.8152 (ttt90) REVERT: D 772 ASN cc_start: 0.7290 (p0) cc_final: 0.7001 (p0) REVERT: D 848 MET cc_start: 0.1624 (mmp) cc_final: 0.1290 (tpt) REVERT: D 870 GLN cc_start: 0.7523 (pt0) cc_final: 0.7101 (pp30) REVERT: D 892 TYR cc_start: 0.8282 (m-10) cc_final: 0.7887 (m-10) REVERT: D 977 GLU cc_start: 0.7945 (tp30) cc_final: 0.7590 (tm-30) REVERT: D 1036 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7367 (tt0) outliers start: 46 outliers final: 15 residues processed: 287 average time/residue: 0.5368 time to fit residues: 179.0831 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 : 0.724 ------------------------------------------------------------------------------- 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 504 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1504 CYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain B residue 247 MET 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 1036 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 10 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 727 HIS A1357 ASN A1429 GLN A1589 GLN A1725 ASN D 108 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 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.178334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119251 restraints weight = 27092.861| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.50 r_work: 0.3229 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 20803 Z= 0.172 Angle : 0.678 13.531 28221 Z= 0.339 Chirality : 0.046 0.246 3199 Planarity : 0.004 0.076 3479 Dihedral : 10.339 102.786 3808 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 2.29 % Allowed : 16.15 % Favored : 81.56 % 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 are not related in a simple way. whole: -1.15 (0.17), residues: 2414 helix: 0.14 (0.15), residues: 1182 sheet: -1.77 (0.33), residues: 218 loop : -1.54 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 230 TYR 0.028 0.001 TYR D 426 PHE 0.020 0.001 PHE D 780 TRP 0.016 0.001 TRP D 185 HIS 0.010 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (20775) covalent geometry : angle 0.66005 / 0.33 (28148) SS BOND : bond 0.00209 / 0.11 ( 11) SS BOND : angle 2.54194 / 1.79 ( 22) hydrogen bonds : bond 0.03890 / 2.52 ( 923) hydrogen bonds : angle 4.71895 / 3.31 ( 2622) link_BETA1-3 : bond 0.00753 / 0.40 ( 1) link_BETA1-3 : angle 4.68594 / 2.93 ( 3) link_BETA1-4 : bond 0.00705 / 0.40 ( 5) link_BETA1-4 : angle 2.50167 / 1.76 ( 15) link_NAG-ASN : bond 0.00475 / 0.23 ( 11) link_NAG-ASN : angle 3.43940 / 2.10 ( 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 299 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 373 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 504 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 530 MET cc_start: 0.7490 (tmm) cc_final: 0.7218 (tmt) REVERT: A 719 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 1157 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7348 (tmt) REVERT: A 1167 SER cc_start: 0.9136 (m) cc_final: 0.8912 (m) REVERT: A 1205 MET cc_start: 0.5302 (mmt) cc_final: 0.5043 (mpp) REVERT: A 1472 TRP cc_start: 0.7615 (t60) cc_final: 0.7237 (t60) REVERT: A 1484 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 1793 MET cc_start: 0.6228 (ppp) cc_final: 0.5771 (ppp) REVERT: A 1810 MET cc_start: 0.7916 (mmt) cc_final: 0.7685 (mpp) REVERT: B 354 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7363 (mtt180) REVERT: D 64 TYR cc_start: 0.8089 (m-80) cc_final: 0.7032 (m-80) REVERT: D 191 GLU cc_start: 0.8052 (pp20) cc_final: 0.7833 (pp20) REVERT: D 246 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8654 (tm-30) REVERT: D 366 GLU cc_start: 0.7232 (tt0) cc_final: 0.6821 (mm-30) REVERT: D 526 ASN cc_start: 0.9005 (t0) cc_final: 0.8696 (t0) REVERT: D 595 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 653 PHE cc_start: 0.6883 (m-80) cc_final: 0.6176 (m-80) REVERT: D 744 TYR cc_start: 0.7477 (t80) cc_final: 0.7263 (t80) REVERT: D 772 ASN cc_start: 0.7263 (p0) cc_final: 0.6959 (p0) REVERT: D 848 MET cc_start: 0.1917 (mmp) cc_final: 0.1492 (tpt) REVERT: D 870 GLN cc_start: 0.7551 (pt0) cc_final: 0.7215 (pp30) REVERT: D 977 GLU cc_start: 0.7825 (tp30) cc_final: 0.7621 (mm-30) outliers start: 49 outliers final: 22 residues processed: 283 average time/residue: 0.5155 time to fit residues: 170.7781 Evaluate side-chains 261 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 473 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1158 CYS 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 B residue 353 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 515 ILE 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: 4.9990 chunk 46 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 727 HIS A1589 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.178311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116277 restraints weight = 26878.839| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.14 r_work: 0.3250 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 20803 Z= 0.176 Angle : 0.663 13.440 28221 Z= 0.333 Chirality : 0.046 0.241 3199 Planarity : 0.004 0.075 3479 Dihedral : 9.900 102.323 3808 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 2.57 % Allowed : 17.41 % Favored : 80.02 % 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 are not related in a simple way. whole: -0.99 (0.17), residues: 2414 helix: 0.28 (0.15), residues: 1183 sheet: -1.62 (0.33), residues: 230 loop : -1.50 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 766 TYR 0.016 0.001 TYR D1068 PHE 0.027 0.002 PHE A1480 TRP 0.016 0.001 TRP D 185 HIS 0.009 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (20775) covalent geometry : angle 0.64806 / 0.33 (28148) SS BOND : bond 0.00211 / 0.11 ( 11) SS BOND : angle 1.89197 / 1.49 ( 22) hydrogen bonds : bond 0.03810 / 2.46 ( 923) hydrogen bonds : angle 4.63545 / 3.25 ( 2622) link_BETA1-3 : bond 0.00803 / 0.42 ( 1) link_BETA1-3 : angle 4.25393 / 2.61 ( 3) link_BETA1-4 : bond 0.00641 / 0.36 ( 5) link_BETA1-4 : angle 2.33776 / 1.67 ( 15) link_NAG-ASN : bond 0.00480 / 0.24 ( 11) link_NAG-ASN : angle 3.37014 / 2.05 ( 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 304 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 472 MET cc_start: 0.4634 (OUTLIER) cc_final: 0.4266 (tmt) REVERT: A 504 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (tp) REVERT: A 530 MET cc_start: 0.7512 (tmm) cc_final: 0.7255 (tmt) REVERT: A 719 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 1157 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7375 (tmt) REVERT: A 1167 SER cc_start: 0.9131 (m) cc_final: 0.8919 (m) REVERT: A 1205 MET cc_start: 0.5264 (mmt) cc_final: 0.4989 (mpp) REVERT: A 1274 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7790 (mtmt) REVERT: A 1429 GLN cc_start: 0.6905 (mp10) cc_final: 0.6396 (pp30) REVERT: A 1793 MET cc_start: 0.6250 (ppp) cc_final: 0.5805 (ppp) REVERT: A 1795 MET cc_start: 0.5105 (pp-130) cc_final: 0.4869 (pp-130) REVERT: A 1810 MET cc_start: 0.7786 (mmt) cc_final: 0.7532 (mpp) REVERT: A 1836 GLN cc_start: 0.7253 (tp-100) cc_final: 0.6516 (mt0) REVERT: B 357 LYS cc_start: 0.8098 (mppt) cc_final: 0.7889 (mmtm) REVERT: D 64 TYR cc_start: 0.8070 (m-80) cc_final: 0.7058 (m-80) REVERT: D 191 GLU cc_start: 0.8020 (pp20) cc_final: 0.7813 (pp20) REVERT: D 197 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.6968 (tmm-80) REVERT: D 366 GLU cc_start: 0.7139 (tt0) cc_final: 0.6791 (mm-30) REVERT: D 526 ASN cc_start: 0.8994 (t0) cc_final: 0.8693 (t0) REVERT: D 595 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 653 PHE cc_start: 0.6889 (m-80) cc_final: 0.6299 (m-80) REVERT: D 744 TYR cc_start: 0.7462 (t80) cc_final: 0.7251 (t80) REVERT: D 772 ASN cc_start: 0.7182 (p0) cc_final: 0.6887 (p0) REVERT: D 793 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7254 (ttm) REVERT: D 801 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: D 848 MET cc_start: 0.1746 (mmp) cc_final: 0.1370 (tpt) REVERT: D 870 GLN cc_start: 0.7500 (pt0) cc_final: 0.7135 (pp30) REVERT: D 977 GLU cc_start: 0.7765 (tp30) cc_final: 0.7526 (mm-30) outliers start: 55 outliers final: 28 residues processed: 287 average time/residue: 0.5053 time to fit residues: 169.5142 Evaluate side-chains 267 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 504 LEU 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 1274 LYS 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 353 GLN 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 393 ASN Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 515 ILE 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 801 TYR Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU 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: 1.9990 chunk 241 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 190 optimal weight: 0.0570 chunk 231 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 727 HIS A1589 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121043 restraints weight = 26791.550| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.45 r_work: 0.3282 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2395 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= 0.121 Angle : 0.619 13.460 28221 Z= 0.310 Chirality : 0.044 0.218 3199 Planarity : 0.004 0.077 3479 Dihedral : 9.507 101.539 3808 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.43 % Allowed : 18.30 % Favored : 79.27 % 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 are not related in a simple way. whole: -0.77 (0.18), residues: 2414 helix: 0.53 (0.15), residues: 1189 sheet: -1.63 (0.33), residues: 234 loop : -1.46 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 766 TYR 0.028 0.001 TYR D 426 PHE 0.029 0.001 PHE D 780 TRP 0.018 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (20775) covalent geometry : angle 0.60488 / 0.31 (28148) SS BOND : bond 0.00200 / 0.11 ( 11) SS BOND : angle 1.34629 / 1.11 ( 22) hydrogen bonds : bond 0.03425 / 2.22 ( 923) hydrogen bonds : angle 4.47415 / 3.13 ( 2622) link_BETA1-3 : bond 0.00802 / 0.42 ( 1) link_BETA1-3 : angle 3.94631 / 2.45 ( 3) link_BETA1-4 : bond 0.00589 / 0.33 ( 5) link_BETA1-4 : angle 2.13875 / 1.52 ( 15) link_NAG-ASN : bond 0.00511 / 0.24 ( 11) link_NAG-ASN : angle 3.29608 / 1.98 ( 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 316 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.795 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: 0.8048 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 138 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6564 (tt0) REVERT: A 215 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6335 (tmt) REVERT: A 365 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8178 (ptp-110) REVERT: A 373 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 472 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.4043 (tmt) REVERT: A 504 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 518 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7311 (tt) REVERT: A 584 LYS cc_start: 0.8373 (pttm) cc_final: 0.7507 (pmmt) REVERT: A 719 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 1156 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7093 (pm20) REVERT: A 1167 SER cc_start: 0.9108 (m) cc_final: 0.8901 (m) REVERT: A 1205 MET cc_start: 0.5244 (mmt) cc_final: 0.4934 (mpp) REVERT: A 1429 GLN cc_start: 0.6915 (mp10) cc_final: 0.6376 (pp30) REVERT: A 1433 MET cc_start: 0.4539 (ppp) cc_final: 0.2437 (mmm) REVERT: A 1504 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5712 (m) REVERT: A 1793 MET cc_start: 0.6309 (ppp) cc_final: 0.5888 (ppp) REVERT: A 1795 MET cc_start: 0.5198 (OUTLIER) cc_final: 0.4922 (pp-130) REVERT: A 1810 MET cc_start: 0.7802 (mmt) cc_final: 0.7505 (mpp) REVERT: A 1836 GLN cc_start: 0.7246 (tp-100) cc_final: 0.6533 (mt0) REVERT: B 230 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6492 (mtm-85) REVERT: B 247 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7068 (mtt) REVERT: B 357 LYS cc_start: 0.8011 (mppt) cc_final: 0.7810 (mppt) REVERT: B 389 LEU cc_start: 0.6171 (mt) cc_final: 0.5856 (tt) REVERT: B 405 LEU cc_start: 0.5823 (mm) cc_final: 0.5289 (pp) REVERT: D 64 TYR cc_start: 0.8068 (m-80) cc_final: 0.7088 (m-80) REVERT: D 191 GLU cc_start: 0.8062 (pp20) cc_final: 0.7858 (pp20) REVERT: D 197 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6920 (tmm-80) REVERT: D 287 ASP cc_start: 0.8414 (m-30) cc_final: 0.8099 (m-30) REVERT: D 366 GLU cc_start: 0.7160 (tt0) cc_final: 0.6842 (mm-30) REVERT: D 461 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8799 (p) REVERT: D 526 ASN cc_start: 0.8971 (t0) cc_final: 0.8655 (t0) REVERT: D 589 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7865 (mtp85) REVERT: D 595 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 653 PHE cc_start: 0.6855 (m-80) cc_final: 0.6267 (m-80) REVERT: D 744 TYR cc_start: 0.7430 (t80) cc_final: 0.7209 (t80) REVERT: D 772 ASN cc_start: 0.7126 (p0) cc_final: 0.6834 (p0) REVERT: D 848 MET cc_start: 0.1666 (mmp) cc_final: 0.1316 (tpt) REVERT: D 870 GLN cc_start: 0.7488 (pt0) cc_final: 0.7159 (pp30) outliers start: 52 outliers final: 24 residues processed: 297 average time/residue: 0.5240 time to fit residues: 181.7317 Evaluate side-chains 273 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 472 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 518 LEU 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 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 1795 MET Chi-restraints excluded: chain B residue 247 MET 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 197 ARG 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 812 VAL Chi-restraints excluded: chain D residue 979 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 HIS A1589 GLN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122684 restraints weight = 26997.003| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.49 r_work: 0.3267 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 20803 Z= 0.130 Angle : 0.631 13.334 28221 Z= 0.316 Chirality : 0.044 0.231 3199 Planarity : 0.004 0.078 3479 Dihedral : 9.314 101.196 3808 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 2.52 % Allowed : 19.61 % Favored : 77.87 % 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 are not related in a simple way. whole: -0.65 (0.18), residues: 2414 helix: 0.62 (0.15), residues: 1203 sheet: -1.62 (0.33), residues: 236 loop : -1.41 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1444 TYR 0.015 0.001 TYR A1765 PHE 0.032 0.001 PHE A1480 TRP 0.015 0.001 TRP D 185 HIS 0.008 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20775) covalent geometry : angle 0.61820 / 0.31 (28148) SS BOND : bond 0.00149 / 0.08 ( 11) SS BOND : angle 1.23456 / 1.07 ( 22) hydrogen bonds : bond 0.03429 / 2.22 ( 923) hydrogen bonds : angle 4.41674 / 3.10 ( 2622) link_BETA1-3 : bond 0.00897 / 0.47 ( 1) link_BETA1-3 : angle 3.81653 / 2.36 ( 3) link_BETA1-4 : bond 0.00573 / 0.31 ( 5) link_BETA1-4 : angle 2.05541 / 1.46 ( 15) link_NAG-ASN : bond 0.00510 / 0.24 ( 11) link_NAG-ASN : angle 3.26157 / 1.96 ( 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 311 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6676 (tt0) REVERT: A 215 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6278 (tmt) REVERT: A 365 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8101 (ptp-110) REVERT: A 373 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 518 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 522 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: A 530 MET cc_start: 0.7354 (tmm) cc_final: 0.7123 (tmt) REVERT: A 584 LYS cc_start: 0.8374 (pttm) cc_final: 0.7516 (pmmt) REVERT: A 719 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 1156 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7029 (pm20) REVERT: A 1157 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7266 (tmt) REVERT: A 1167 SER cc_start: 0.9116 (m) cc_final: 0.8909 (m) REVERT: A 1205 MET cc_start: 0.5238 (mmt) cc_final: 0.4941 (mpp) REVERT: A 1429 GLN cc_start: 0.6907 (mp10) cc_final: 0.6344 (pp30) REVERT: A 1434 MET cc_start: 0.2734 (tmm) cc_final: 0.2414 (ttp) REVERT: A 1472 TRP cc_start: 0.7571 (t60) cc_final: 0.6778 (t-100) REVERT: A 1504 CYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5669 (m) REVERT: A 1793 MET cc_start: 0.6215 (ppp) cc_final: 0.5786 (ppp) REVERT: A 1795 MET cc_start: 0.5167 (pp-130) cc_final: 0.4885 (pp-130) REVERT: A 1836 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6460 (mt0) REVERT: B 247 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7112 (mtt) REVERT: B 357 LYS cc_start: 0.7917 (mppt) cc_final: 0.7677 (mmtm) REVERT: B 389 LEU cc_start: 0.6091 (mt) cc_final: 0.5821 (tt) REVERT: B 405 LEU cc_start: 0.5772 (mm) cc_final: 0.5276 (pp) REVERT: D 64 TYR cc_start: 0.8020 (m-80) cc_final: 0.6960 (m-80) REVERT: D 191 GLU cc_start: 0.8100 (pp20) cc_final: 0.7896 (pp20) REVERT: D 197 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6868 (tmm-80) REVERT: D 287 ASP cc_start: 0.8526 (m-30) cc_final: 0.8291 (m-30) REVERT: D 366 GLU cc_start: 0.7143 (tt0) cc_final: 0.6887 (mm-30) REVERT: D 526 ASN cc_start: 0.9003 (t0) cc_final: 0.8656 (t0) REVERT: D 589 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7830 (mtp85) REVERT: D 595 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 653 PHE cc_start: 0.6860 (m-80) cc_final: 0.6248 (m-80) REVERT: D 678 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8681 (tm-30) REVERT: D 744 TYR cc_start: 0.7459 (t80) cc_final: 0.7204 (t80) REVERT: D 772 ASN cc_start: 0.7204 (p0) cc_final: 0.6896 (p0) REVERT: D 848 MET cc_start: 0.1512 (mmp) cc_final: 0.1284 (tpt) REVERT: D 870 GLN cc_start: 0.7612 (pt0) cc_final: 0.7237 (pp30) REVERT: D 1017 MET cc_start: 0.5372 (pmm) cc_final: 0.5127 (pmt) outliers start: 54 outliers final: 25 residues processed: 290 average time/residue: 0.5230 time to fit residues: 177.2732 Evaluate side-chains 273 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 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 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 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 B residue 247 MET 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 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 515 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 241 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 194 optimal weight: 0.0050 chunk 148 optimal weight: 5.9990 chunk 227 optimal weight: 0.0770 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 HIS A1589 GLN D 481 ASN D 554 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.183181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123635 restraints weight = 26961.863| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.46 r_work: 0.3316 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 20803 Z= 0.109 Angle : 0.614 13.281 28221 Z= 0.305 Chirality : 0.043 0.207 3199 Planarity : 0.004 0.079 3479 Dihedral : 9.040 100.603 3808 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 2.47 % Allowed : 20.26 % Favored : 77.26 % 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 are not related in a simple way. whole: -0.48 (0.18), residues: 2414 helix: 0.81 (0.16), residues: 1199 sheet: -1.65 (0.34), residues: 220 loop : -1.36 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 766 TYR 0.023 0.001 TYR D 426 PHE 0.026 0.001 PHE A1480 TRP 0.017 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20775) covalent geometry : angle 0.60149 / 0.30 (28148) SS BOND : bond 0.00133 / 0.08 ( 11) SS BOND : angle 1.00979 / 0.86 ( 22) hydrogen bonds : bond 0.03207 / 2.09 ( 923) hydrogen bonds : angle 4.29611 / 3.00 ( 2622) link_BETA1-3 : bond 0.00837 / 0.44 ( 1) link_BETA1-3 : angle 3.70059 / 2.29 ( 3) link_BETA1-4 : bond 0.00610 / 0.36 ( 5) link_BETA1-4 : angle 1.90823 / 1.34 ( 15) link_NAG-ASN : bond 0.00535 / 0.25 ( 11) link_NAG-ASN : angle 3.18941 / 1.91 ( 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 314 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 0.789 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: 0.8062 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 215 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6405 (tmt) REVERT: A 365 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8204 (ptp-110) REVERT: A 373 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 522 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: A 530 MET cc_start: 0.7464 (tmm) cc_final: 0.7248 (tmt) REVERT: A 719 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 1156 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7034 (pm20) REVERT: A 1167 SER cc_start: 0.9036 (m) cc_final: 0.8747 (m) REVERT: A 1205 MET cc_start: 0.5240 (mmt) cc_final: 0.4940 (mpp) REVERT: A 1433 MET cc_start: 0.4576 (ppp) cc_final: 0.2546 (mmm) REVERT: A 1434 MET cc_start: 0.2647 (tmm) cc_final: 0.2405 (ttp) REVERT: A 1472 TRP cc_start: 0.7530 (t60) cc_final: 0.6788 (t-100) REVERT: A 1793 MET cc_start: 0.6112 (ppp) cc_final: 0.5697 (ppp) REVERT: A 1795 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.5045 (pp-130) REVERT: A 1836 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6469 (mt0) REVERT: A 1857 MET cc_start: 0.4708 (ttp) cc_final: 0.4500 (ttp) REVERT: B 357 LYS cc_start: 0.8046 (mppt) cc_final: 0.7781 (mmtm) REVERT: B 367 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.7015 (mt) REVERT: B 383 GLU cc_start: 0.4692 (pm20) cc_final: 0.4338 (pp20) REVERT: B 389 LEU cc_start: 0.6011 (mt) cc_final: 0.5779 (tt) REVERT: B 391 GLU cc_start: 0.7164 (pt0) cc_final: 0.5923 (pp20) REVERT: B 405 LEU cc_start: 0.6055 (mm) cc_final: 0.5560 (pp) REVERT: D 64 TYR cc_start: 0.8012 (m-80) cc_final: 0.7028 (m-80) REVERT: D 287 ASP cc_start: 0.8463 (m-30) cc_final: 0.8208 (m-30) REVERT: D 366 GLU cc_start: 0.7046 (tt0) cc_final: 0.6806 (mm-30) REVERT: D 482 GLN cc_start: 0.8261 (mt0) cc_final: 0.7747 (mp10) REVERT: D 516 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: D 526 ASN cc_start: 0.8977 (t0) cc_final: 0.8652 (t0) REVERT: D 589 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7720 (mtp85) REVERT: D 595 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 653 PHE cc_start: 0.6755 (m-80) cc_final: 0.6163 (m-80) REVERT: D 678 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8641 (tm-30) REVERT: D 744 TYR cc_start: 0.7466 (t80) cc_final: 0.7230 (t80) REVERT: D 772 ASN cc_start: 0.7232 (p0) cc_final: 0.6899 (p0) REVERT: D 848 MET cc_start: 0.1513 (mmp) cc_final: 0.1251 (tpt) REVERT: D 870 GLN cc_start: 0.7612 (pt0) cc_final: 0.7270 (pp30) REVERT: D 1017 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.5046 (pmm) outliers start: 53 outliers final: 25 residues processed: 293 average time/residue: 0.5098 time to fit residues: 174.7216 Evaluate side-chains 278 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1384 VAL 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 A residue 1795 MET Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL 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 481 ASN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 516 ASP 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 882 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1017 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122286 restraints weight = 26840.390| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.51 r_work: 0.3284 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2813 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= 0.132 Angle : 0.625 13.196 28221 Z= 0.311 Chirality : 0.044 0.213 3199 Planarity : 0.004 0.079 3479 Dihedral : 8.991 100.921 3808 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.92 % Favored : 93.04 % Rotamer: Outliers : 2.19 % Allowed : 21.06 % Favored : 76.75 % 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 are not related in a simple way. whole: -0.42 (0.18), residues: 2414 helix: 0.83 (0.15), residues: 1202 sheet: -1.60 (0.33), residues: 226 loop : -1.29 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1789 TYR 0.021 0.001 TYR D1068 PHE 0.025 0.001 PHE A1480 TRP 0.014 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (20775) covalent geometry : angle 0.61283 / 0.31 (28148) SS BOND : bond 0.00159 / 0.09 ( 11) SS BOND : angle 1.11790 / 0.97 ( 22) hydrogen bonds : bond 0.03330 / 2.15 ( 923) hydrogen bonds : angle 4.30225 / 3.01 ( 2622) link_BETA1-3 : bond 0.00884 / 0.47 ( 1) link_BETA1-3 : angle 3.65360 / 2.25 ( 3) link_BETA1-4 : bond 0.00608 / 0.35 ( 5) link_BETA1-4 : angle 1.88714 / 1.33 ( 15) link_NAG-ASN : bond 0.00522 / 0.25 ( 11) link_NAG-ASN : angle 3.17203 / 1.91 ( 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 295 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.721 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: 0.8108 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 215 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6384 (tmt) REVERT: A 365 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8172 (ptp-110) REVERT: A 373 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 522 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: A 530 MET cc_start: 0.7477 (tmm) cc_final: 0.7256 (tmt) REVERT: A 719 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 1156 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6923 (pm20) REVERT: A 1167 SER cc_start: 0.9064 (m) cc_final: 0.8795 (m) REVERT: A 1205 MET cc_start: 0.5292 (mmt) cc_final: 0.4955 (mpp) REVERT: A 1472 TRP cc_start: 0.7561 (t60) cc_final: 0.6844 (t-100) REVERT: A 1793 MET cc_start: 0.6074 (ppp) cc_final: 0.5666 (ppp) REVERT: A 1795 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.5035 (pp-130) REVERT: A 1836 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6415 (mt0) REVERT: B 357 LYS cc_start: 0.8157 (mppt) cc_final: 0.7857 (mmtm) REVERT: B 367 LEU cc_start: 0.7250 (tm) cc_final: 0.6965 (mt) REVERT: B 383 GLU cc_start: 0.4739 (pm20) cc_final: 0.4374 (pp20) REVERT: B 391 GLU cc_start: 0.7157 (pt0) cc_final: 0.6532 (pm20) REVERT: B 405 LEU cc_start: 0.6012 (mm) cc_final: 0.5587 (pp) REVERT: D 64 TYR cc_start: 0.8006 (m-80) cc_final: 0.7016 (m-80) REVERT: D 287 ASP cc_start: 0.8522 (m-30) cc_final: 0.8315 (m-30) REVERT: D 366 GLU cc_start: 0.7082 (tt0) cc_final: 0.6856 (mm-30) REVERT: D 482 GLN cc_start: 0.8337 (mt0) cc_final: 0.7820 (mp10) REVERT: D 516 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: D 526 ASN cc_start: 0.9000 (t0) cc_final: 0.8662 (t0) REVERT: D 589 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7697 (mtp85) REVERT: D 595 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8077 (tm-30) REVERT: D 653 PHE cc_start: 0.6802 (m-80) cc_final: 0.6193 (m-80) REVERT: D 744 TYR cc_start: 0.7497 (t80) cc_final: 0.7264 (t80) REVERT: D 772 ASN cc_start: 0.7099 (p0) cc_final: 0.6760 (p0) REVERT: D 848 MET cc_start: 0.1555 (mmp) cc_final: 0.1348 (tpt) REVERT: D 870 GLN cc_start: 0.7557 (pt0) cc_final: 0.7235 (pp30) REVERT: D 1017 MET cc_start: 0.5352 (OUTLIER) cc_final: 0.5000 (pmm) outliers start: 47 outliers final: 32 residues processed: 279 average time/residue: 0.4919 time to fit residues: 160.7165 Evaluate side-chains 276 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 522 GLU 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 775 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 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 A residue 1795 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 207 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1017 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 54 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122998 restraints weight = 26980.503| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.57 r_work: 0.3277 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 20803 Z= 0.137 Angle : 0.629 13.142 28221 Z= 0.312 Chirality : 0.044 0.214 3199 Planarity : 0.004 0.080 3479 Dihedral : 8.996 101.542 3808 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 1.87 % Allowed : 21.57 % Favored : 76.56 % 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 are not related in a simple way. whole: -0.39 (0.18), residues: 2414 helix: 0.85 (0.15), residues: 1201 sheet: -1.59 (0.33), residues: 220 loop : -1.28 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1789 TYR 0.023 0.001 TYR D 426 PHE 0.024 0.001 PHE A1480 TRP 0.014 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (20775) covalent geometry : angle 0.61695 / 0.31 (28148) SS BOND : bond 0.00168 / 0.09 ( 11) SS BOND : angle 1.11298 / 0.97 ( 22) hydrogen bonds : bond 0.03369 / 2.17 ( 923) hydrogen bonds : angle 4.29118 / 3.00 ( 2622) link_BETA1-3 : bond 0.00890 / 0.47 ( 1) link_BETA1-3 : angle 3.56739 / 2.20 ( 3) link_BETA1-4 : bond 0.00608 / 0.35 ( 5) link_BETA1-4 : angle 1.85050 / 1.30 ( 15) link_NAG-ASN : bond 0.00505 / 0.24 ( 11) link_NAG-ASN : angle 3.16550 / 1.91 ( 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 285 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: A 365 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8167 (ptp-110) REVERT: A 373 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 530 MET cc_start: 0.7472 (tmm) cc_final: 0.7240 (tmt) REVERT: A 719 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 1156 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6989 (pm20) REVERT: A 1167 SER cc_start: 0.9094 (m) cc_final: 0.8867 (m) REVERT: A 1205 MET cc_start: 0.5299 (mmt) cc_final: 0.4964 (mpp) REVERT: A 1433 MET cc_start: 0.4089 (ppp) cc_final: 0.2052 (mmm) REVERT: A 1472 TRP cc_start: 0.7560 (t60) cc_final: 0.6882 (t-100) REVERT: A 1487 MET cc_start: 0.8307 (tpp) cc_final: 0.8094 (mmp) REVERT: A 1793 MET cc_start: 0.6149 (ppp) cc_final: 0.5749 (ppp) REVERT: A 1795 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.5031 (pp-130) REVERT: A 1836 GLN cc_start: 0.7171 (tp-100) cc_final: 0.6416 (mt0) REVERT: B 357 LYS cc_start: 0.8171 (mppt) cc_final: 0.7871 (mmtm) REVERT: B 367 LEU cc_start: 0.7216 (tm) cc_final: 0.6964 (mt) REVERT: B 383 GLU cc_start: 0.4732 (pm20) cc_final: 0.4365 (pp20) REVERT: B 405 LEU cc_start: 0.6099 (mm) cc_final: 0.5655 (pp) REVERT: D 64 TYR cc_start: 0.8008 (m-80) cc_final: 0.7008 (m-80) REVERT: D 366 GLU cc_start: 0.7034 (tt0) cc_final: 0.6833 (mm-30) REVERT: D 482 GLN cc_start: 0.8282 (mt0) cc_final: 0.7804 (mp10) REVERT: D 516 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: D 526 ASN cc_start: 0.9002 (t0) cc_final: 0.8669 (t0) REVERT: D 589 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7702 (mtp85) REVERT: D 595 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8055 (tm-30) REVERT: D 653 PHE cc_start: 0.6844 (m-80) cc_final: 0.6236 (m-80) REVERT: D 744 TYR cc_start: 0.7517 (t80) cc_final: 0.7285 (t80) REVERT: D 772 ASN cc_start: 0.7076 (p0) cc_final: 0.6742 (p0) REVERT: D 848 MET cc_start: 0.1584 (mmp) cc_final: 0.1374 (tpt) REVERT: D 870 GLN cc_start: 0.7539 (pt0) cc_final: 0.7230 (pp30) REVERT: D 1017 MET cc_start: 0.5446 (OUTLIER) cc_final: 0.5070 (pmm) outliers start: 40 outliers final: 31 residues processed: 271 average time/residue: 0.5058 time to fit residues: 160.8607 Evaluate side-chains 272 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 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 A residue 1795 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 207 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 516 ASP 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 1017 MET 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: 30.0000 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120283 restraints weight = 26972.938| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.56 r_work: 0.3266 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 20803 Z= 0.148 Angle : 0.645 15.964 28221 Z= 0.318 Chirality : 0.045 0.215 3199 Planarity : 0.004 0.081 3479 Dihedral : 9.020 102.080 3808 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.05 % Allowed : 21.71 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2414 helix: 0.83 (0.15), residues: 1202 sheet: -1.61 (0.33), residues: 226 loop : -1.27 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1789 TYR 0.025 0.001 TYR D1068 PHE 0.024 0.001 PHE A1480 TRP 0.014 0.001 TRP D 185 HIS 0.007 0.001 HIS A1760 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (20775) covalent geometry : angle 0.63361 / 0.32 (28148) SS BOND : bond 0.00178 / 0.09 ( 11) SS BOND : angle 1.16348 / 1.01 ( 22) hydrogen bonds : bond 0.03422 / 2.20 ( 923) hydrogen bonds : angle 4.30158 / 3.01 ( 2622) link_BETA1-3 : bond 0.00872 / 0.46 ( 1) link_BETA1-3 : angle 3.51879 / 2.16 ( 3) link_BETA1-4 : bond 0.00582 / 0.34 ( 5) link_BETA1-4 : angle 1.82108 / 1.28 ( 15) link_NAG-ASN : bond 0.00501 / 0.24 ( 11) link_NAG-ASN : angle 3.17351 / 1.91 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8334.34 seconds wall clock time: 142 minutes 31.14 seconds (8551.14 seconds total)