Starting phenix.real_space_refine on Mon Mar 11 15:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/03_2024/6kzp_0792.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 P 5 5.49 5 S 65 5.16 5 Cl 1 4.86 5 C 5694 2.51 5 N 1336 2.21 5 O 1453 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1284": "NH1" <-> "NH2" Residue "A ARG 1355": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1361": "NH1" <-> "NH2" Residue "A ARG 1364": "NH1" <-> "NH2" Residue "A ARG 1367": "NH1" <-> "NH2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A ARG 1646": "NH1" <-> "NH2" Residue "A ARG 1651": "NH1" <-> "NH2" Residue "A ARG 1686": "NH1" <-> "NH2" Residue "A ARG 1689": "NH1" <-> "NH2" Residue "A ARG 1692": "NH1" <-> "NH2" Residue "A ARG 1763": "NH1" <-> "NH2" Residue "A ARG 1790": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8557 Unusual residues: {' CA': 2, '3PE': 8, 'DZR': 1, 'NAG': 4, 'Y01': 3} Classifications: {'peptide': 1014, 'undetermined': 18} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 985, None: 18} Not linked: pdbres="LYS A1836 " pdbres=" CA A2301 " Not linked: pdbres=" CA A2301 " pdbres=" CA A2302 " Not linked: pdbres=" CA A2302 " pdbres="NAG A2303 " Not linked: pdbres="NAG A2303 " pdbres="NAG A2304 " Not linked: pdbres="NAG A2304 " pdbres="NAG A2305 " ... (remaining 13 not shown) Chain breaks: 10 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, '3PE:plan-1': 3, '3PE:plan-2': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 5.25, per 1000 atoms: 0.61 Number of scatterers: 8557 At special positions: 0 Unit cell: (108.009, 121.101, 104.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 2 19.99 Cl 1 17.00 S 65 16.00 P 5 15.00 F 1 9.00 O 1453 8.00 N 1336 7.00 C 5694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 282 " distance=2.04 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1432 " distance=2.03 Simple disulfide: pdb=" SG CYS A1747 " - pdb=" SG CYS A1753 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A2303 " - " ASN A 246 " " NAG A2304 " - " ASN A 322 " " NAG A2305 " - " ASN A1425 " " NAG A2306 " - " ASN A1428 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 78.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.971A pdb=" N GLU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 136 Processing helix chain 'A' and resid 151 through 172 removed outlier: 3.853A pdb=" N VAL A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.674A pdb=" N ARG A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.737A pdb=" N ILE A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 234 removed outlier: 3.607A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.938A pdb=" N VAL A 285 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.187A pdb=" N GLN A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 320 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.507A pdb=" N TRP A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.781A pdb=" N ILE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.743A pdb=" N PHE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.604A pdb=" N LEU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 761 removed outlier: 3.556A pdb=" N MET A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 754 " --> pdb=" O MET A 750 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 760 " --> pdb=" O ASN A 756 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.546A pdb=" N LEU A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.525A pdb=" N ILE A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 823 removed outlier: 3.841A pdb=" N ILE A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.619A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 836' Processing helix chain 'A' and resid 837 through 845 removed outlier: 3.538A pdb=" N ARG A 840 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 844 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 845 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 865 removed outlier: 3.593A pdb=" N MET A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 887 removed outlier: 3.532A pdb=" N LEU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.643A pdb=" N THR A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 removed outlier: 3.708A pdb=" N VAL A 928 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 940 through 953 removed outlier: 4.223A pdb=" N PHE A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 968 removed outlier: 3.717A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.605A pdb=" N ARG A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A1250 " --> pdb=" O CYS A1246 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1272 removed outlier: 4.135A pdb=" N ASP A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A1257 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A1260 " --> pdb=" O ASP A1256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1268 " --> pdb=" O PHE A1264 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1309 removed outlier: 3.612A pdb=" N ASN A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A1292 " --> pdb=" O THR A1288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A1297 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A1307 " --> pdb=" O THR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1344 removed outlier: 3.503A pdb=" N VAL A1331 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1362 removed outlier: 3.895A pdb=" N VAL A1356 " --> pdb=" O GLY A1352 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1357 " --> pdb=" O MET A1353 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1359 " --> pdb=" O ARG A1355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1366 Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.954A pdb=" N ARG A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1386 removed outlier: 3.658A pdb=" N VAL A1378 " --> pdb=" O GLY A1374 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1412 removed outlier: 3.690A pdb=" N ILE A1401 " --> pdb=" O CYS A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1436 removed outlier: 3.809A pdb=" N CYS A1432 " --> pdb=" O ASN A1428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1461 removed outlier: 3.720A pdb=" N MET A1454 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1475 removed outlier: 3.887A pdb=" N ILE A1468 " --> pdb=" O GLY A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1489 No H-bonds generated for 'chain 'A' and resid 1487 through 1489' Processing helix chain 'A' and resid 1490 through 1518 removed outlier: 3.709A pdb=" N SER A1496 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A1515 " --> pdb=" O GLY A1511 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1518 " --> pdb=" O VAL A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1607 removed outlier: 3.687A pdb=" N GLY A1596 " --> pdb=" O LEU A1592 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1643 removed outlier: 3.513A pdb=" N LEU A1620 " --> pdb=" O LEU A1616 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1621 " --> pdb=" O ASP A1617 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1628 " --> pdb=" O ASN A1624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1629 " --> pdb=" O TYR A1625 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1630 " --> pdb=" O ILE A1626 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1634 " --> pdb=" O ILE A1630 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1641 " --> pdb=" O PHE A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1650 removed outlier: 3.553A pdb=" N ASP A1650 " --> pdb=" O ARG A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1668 removed outlier: 3.647A pdb=" N ALA A1658 " --> pdb=" O GLN A1654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1668 " --> pdb=" O ILE A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1676 removed outlier: 3.919A pdb=" N GLU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1692 removed outlier: 3.894A pdb=" N ILE A1685 " --> pdb=" O ASN A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1700 removed outlier: 3.514A pdb=" N VAL A1696 " --> pdb=" O ILE A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 3.597A pdb=" N ALA A1708 " --> pdb=" O VAL A1704 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A1712 " --> pdb=" O ALA A1708 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1713 " --> pdb=" O LEU A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1743 Processing helix chain 'A' and resid 1764 through 1777 Processing helix chain 'A' and resid 1780 through 1789 removed outlier: 3.746A pdb=" N ILE A1784 " --> pdb=" O ASN A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1832 Proline residue: A1805 - end of helix removed outlier: 3.588A pdb=" N PHE A1817 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 1416 through 1419 removed outlier: 3.523A pdb=" N ARG A1438 " --> pdb=" O GLN A1419 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1407 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: 2.42 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1286 1.31 - 1.43: 2335 1.43 - 1.56: 4958 1.56 - 1.69: 43 1.69 - 1.82: 113 Bond restraints: 8735 Sorted by residual: bond pdb=" CAI Y01 A2317 " pdb=" CAZ Y01 A2317 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 A2318 " pdb=" CAZ Y01 A2318 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.16e+02 bond pdb=" CAI Y01 A2316 " pdb=" CAZ Y01 A2316 " ideal model delta sigma weight residual 1.332 1.682 -0.350 2.00e-02 2.50e+03 3.07e+02 bond pdb=" CAP Y01 A2317 " pdb=" CAQ Y01 A2317 " ideal model delta sigma weight residual 1.541 1.728 -0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" CAP Y01 A2318 " pdb=" CAQ Y01 A2318 " ideal model delta sigma weight residual 1.541 1.726 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 8730 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.49: 124 104.49 - 111.92: 4123 111.92 - 119.35: 3065 119.35 - 126.79: 4398 126.79 - 134.22: 96 Bond angle restraints: 11806 Sorted by residual: angle pdb=" O12 3PE A2308 " pdb=" P 3PE A2308 " pdb=" O14 3PE A2308 " ideal model delta sigma weight residual 123.79 99.86 23.93 3.00e+00 1.11e-01 6.36e+01 angle pdb=" O12 3PE A2315 " pdb=" P 3PE A2315 " pdb=" O14 3PE A2315 " ideal model delta sigma weight residual 123.79 100.79 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O12 3PE A2311 " pdb=" P 3PE A2311 " pdb=" O14 3PE A2311 " ideal model delta sigma weight residual 123.79 101.04 22.75 3.00e+00 1.11e-01 5.75e+01 angle pdb=" O12 3PE A2313 " pdb=" P 3PE A2313 " pdb=" O14 3PE A2313 " ideal model delta sigma weight residual 123.79 101.05 22.74 3.00e+00 1.11e-01 5.74e+01 angle pdb=" O12 3PE A2309 " pdb=" P 3PE A2309 " pdb=" O14 3PE A2309 " ideal model delta sigma weight residual 123.79 101.99 21.80 3.00e+00 1.11e-01 5.28e+01 ... (remaining 11801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 5057 24.94 - 49.88: 289 49.88 - 74.83: 52 74.83 - 99.77: 2 99.77 - 124.71: 11 Dihedral angle restraints: 5411 sinusoidal: 2457 harmonic: 2954 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1432 " pdb=" CB CYS A1432 " ideal model delta sinusoidal sigma weight residual -86.00 -152.47 66.47 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" N GLU A 769 " pdb=" C GLU A 769 " pdb=" CA GLU A 769 " pdb=" CB GLU A 769 " ideal model delta harmonic sigma weight residual 122.80 135.02 -12.22 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ASP A 907 " pdb=" C ASP A 907 " pdb=" N SER A 908 " pdb=" CA SER A 908 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1325 0.143 - 0.285: 42 0.285 - 0.428: 13 0.428 - 0.570: 0 0.570 - 0.713: 3 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CBI Y01 A2317 " pdb=" CAU Y01 A2317 " pdb=" CBE Y01 A2317 " pdb=" CBG Y01 A2317 " both_signs ideal model delta sigma weight residual False 2.94 2.22 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CBI Y01 A2318 " pdb=" CAU Y01 A2318 " pdb=" CBE Y01 A2318 " pdb=" CBG Y01 A2318 " both_signs ideal model delta sigma weight residual False 2.94 2.30 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CBI Y01 A2316 " pdb=" CAU Y01 A2316 " pdb=" CBE Y01 A2316 " pdb=" CBG Y01 A2316 " both_signs ideal model delta sigma weight residual False 2.94 2.30 0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1380 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1387 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A1388 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A1388 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1388 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1717 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A1718 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A1718 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1718 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1364 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A1365 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A1365 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1365 " -0.045 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3114 2.89 - 3.39: 8267 3.39 - 3.90: 13070 3.90 - 4.40: 15585 4.40 - 4.90: 25812 Nonbonded interactions: 65848 Sorted by model distance: nonbonded pdb=" O PHE A1403 " pdb=" OH TYR A1493 " model vdw 2.390 2.440 nonbonded pdb=" O SER A1810 " pdb=" OG1 THR A1814 " model vdw 2.430 2.440 nonbonded pdb=" O21 3PE A2311 " pdb=" O31 3PE A2311 " model vdw 2.443 2.432 nonbonded pdb=" O5 NAG A2304 " pdb=" O6 NAG A2304 " model vdw 2.446 2.432 nonbonded pdb=" C12 DZR A2307 " pdb=" O14 3PE A2313 " model vdw 2.458 3.440 ... (remaining 65843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.013 0.357 8735 Z= 0.807 Angle : 1.454 23.926 11806 Z= 0.706 Chirality : 0.077 0.713 1383 Planarity : 0.009 0.102 1414 Dihedral : 16.067 124.710 3475 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.33 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 6.87 % Favored : 90.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.21), residues: 992 helix: -3.17 (0.15), residues: 694 sheet: -4.04 (1.35), residues: 12 loop : -1.83 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 233 HIS 0.009 0.002 HIS A 765 PHE 0.046 0.004 PHE A1403 TYR 0.029 0.004 TYR A 320 ARG 0.012 0.001 ARG A1441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 0.909 Fit side-chains REVERT: A 85 ARG cc_start: 0.7488 (mtt90) cc_final: 0.6958 (mtm180) REVERT: A 92 LEU cc_start: 0.7718 (mm) cc_final: 0.7331 (mp) REVERT: A 118 GLN cc_start: 0.7981 (tt0) cc_final: 0.7134 (tp40) REVERT: A 122 ASP cc_start: 0.5882 (m-30) cc_final: 0.5528 (m-30) REVERT: A 128 PHE cc_start: 0.7973 (m-80) cc_final: 0.7764 (m-10) REVERT: A 183 ARG cc_start: 0.7343 (ptt180) cc_final: 0.7106 (ptt90) REVERT: A 213 ASN cc_start: 0.8189 (m-40) cc_final: 0.7963 (m-40) REVERT: A 263 ASN cc_start: 0.7574 (p0) cc_final: 0.7064 (p0) REVERT: A 835 THR cc_start: 0.8265 (m) cc_final: 0.7917 (p) REVERT: A 859 MET cc_start: 0.6816 (mmt) cc_final: 0.6366 (ptp) REVERT: A 884 MET cc_start: 0.8700 (mtp) cc_final: 0.8477 (mtp) REVERT: A 1243 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7379 (ttt-90) REVERT: A 1383 MET cc_start: 0.7876 (mmt) cc_final: 0.7586 (mmm) REVERT: A 1651 ARG cc_start: 0.6399 (tpp-160) cc_final: 0.5771 (ttp-170) REVERT: A 1719 GLN cc_start: 0.7512 (tp40) cc_final: 0.7166 (tm-30) REVERT: A 1725 LEU cc_start: 0.8218 (tt) cc_final: 0.7831 (mt) outliers start: 22 outliers final: 10 residues processed: 240 average time/residue: 0.2369 time to fit residues: 74.7171 Evaluate side-chains 178 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 864 ASN A 918 GLN A 957 ASN A1252 HIS A1391 ASN A1442 HIS A1624 ASN A1649 GLN A1675 ASN A1681 ASN A1722 ASN A1751 HIS A1780 ASN A1821 ASN A1835 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8735 Z= 0.207 Angle : 0.664 9.537 11806 Z= 0.327 Chirality : 0.043 0.303 1383 Planarity : 0.006 0.073 1414 Dihedral : 14.750 101.420 1600 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 3.22 % Allowed : 11.42 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.23), residues: 992 helix: -0.97 (0.17), residues: 735 sheet: -3.36 (1.41), residues: 12 loop : -1.89 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 911 HIS 0.003 0.001 HIS A1751 PHE 0.016 0.002 PHE A 868 TYR 0.019 0.002 TYR A1437 ARG 0.006 0.001 ARG A1645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 0.911 Fit side-chains REVERT: A 85 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7180 (mtm180) REVERT: A 92 LEU cc_start: 0.7421 (mm) cc_final: 0.7188 (mp) REVERT: A 118 GLN cc_start: 0.7939 (tt0) cc_final: 0.7095 (tp-100) REVERT: A 122 ASP cc_start: 0.5973 (m-30) cc_final: 0.5694 (m-30) REVERT: A 251 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 808 ASN cc_start: 0.8239 (m-40) cc_final: 0.7310 (m110) REVERT: A 835 THR cc_start: 0.8470 (m) cc_final: 0.8220 (p) REVERT: A 859 MET cc_start: 0.6682 (mmt) cc_final: 0.6268 (ptp) REVERT: A 1243 ARG cc_start: 0.7458 (ttt-90) cc_final: 0.7204 (ttt-90) REVERT: A 1353 MET cc_start: 0.7886 (tmm) cc_final: 0.7474 (tpp) REVERT: A 1383 MET cc_start: 0.7743 (mmt) cc_final: 0.7446 (mmm) REVERT: A 1431 ASP cc_start: 0.7465 (t0) cc_final: 0.7182 (t0) REVERT: A 1651 ARG cc_start: 0.6033 (tpp-160) cc_final: 0.5401 (ttt180) REVERT: A 1828 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7403 (mmm) outliers start: 29 outliers final: 15 residues processed: 203 average time/residue: 0.2174 time to fit residues: 59.4951 Evaluate side-chains 176 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1828 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 0.0050 chunk 92 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 885 HIS A1719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8735 Z= 0.182 Angle : 0.611 9.672 11806 Z= 0.292 Chirality : 0.042 0.279 1383 Planarity : 0.005 0.064 1414 Dihedral : 13.262 94.267 1591 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 13.41 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 992 helix: 0.26 (0.19), residues: 737 sheet: -2.78 (1.47), residues: 12 loop : -1.74 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 911 HIS 0.001 0.000 HIS A 328 PHE 0.014 0.001 PHE A 868 TYR 0.012 0.001 TYR A1437 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.046 Fit side-chains REVERT: A 85 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7127 (mtm180) REVERT: A 92 LEU cc_start: 0.7359 (mm) cc_final: 0.7148 (mp) REVERT: A 122 ASP cc_start: 0.6053 (m-30) cc_final: 0.5807 (m-30) REVERT: A 216 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 251 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6961 (mt) REVERT: A 808 ASN cc_start: 0.8136 (m-40) cc_final: 0.7241 (m110) REVERT: A 848 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6809 (pp) REVERT: A 859 MET cc_start: 0.6624 (mmt) cc_final: 0.6135 (ptp) REVERT: A 1243 ARG cc_start: 0.7283 (ttt-90) cc_final: 0.7027 (ttt-90) REVERT: A 1353 MET cc_start: 0.7775 (tmm) cc_final: 0.7527 (tpp) REVERT: A 1389 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7698 (pp) REVERT: A 1651 ARG cc_start: 0.6261 (tpp-160) cc_final: 0.5440 (tmm160) REVERT: A 1692 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7787 (ttm170) outliers start: 35 outliers final: 14 residues processed: 191 average time/residue: 0.2400 time to fit residues: 61.0434 Evaluate side-chains 178 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8735 Z= 0.193 Angle : 0.587 9.707 11806 Z= 0.281 Chirality : 0.042 0.264 1383 Planarity : 0.005 0.064 1414 Dihedral : 12.472 94.942 1589 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 15.41 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 992 helix: 0.82 (0.19), residues: 741 sheet: -2.35 (1.45), residues: 12 loop : -1.65 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 911 HIS 0.002 0.001 HIS A 885 PHE 0.019 0.001 PHE A 127 TYR 0.012 0.001 TYR A 374 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.983 Fit side-chains REVERT: A 85 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7071 (mtm180) REVERT: A 92 LEU cc_start: 0.7424 (mm) cc_final: 0.7172 (mp) REVERT: A 122 ASP cc_start: 0.6103 (m-30) cc_final: 0.5845 (m-30) REVERT: A 216 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8170 (tt) REVERT: A 251 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 808 ASN cc_start: 0.8124 (m-40) cc_final: 0.7352 (m110) REVERT: A 848 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6784 (pp) REVERT: A 859 MET cc_start: 0.6626 (mmt) cc_final: 0.6024 (ptp) REVERT: A 1353 MET cc_start: 0.7764 (tmm) cc_final: 0.7548 (tpp) REVERT: A 1387 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7113 (mttt) REVERT: A 1389 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 1651 ARG cc_start: 0.6326 (tpp-160) cc_final: 0.5421 (tmm160) REVERT: A 1692 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7797 (ttm170) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.2548 time to fit residues: 58.1690 Evaluate side-chains 174 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1719 GLN A1782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8735 Z= 0.286 Angle : 0.651 9.843 11806 Z= 0.311 Chirality : 0.045 0.279 1383 Planarity : 0.005 0.063 1414 Dihedral : 12.600 98.689 1589 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 3.44 % Allowed : 16.19 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 992 helix: 0.92 (0.19), residues: 730 sheet: -1.95 (1.52), residues: 12 loop : -1.45 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 911 HIS 0.003 0.001 HIS A1609 PHE 0.018 0.002 PHE A 868 TYR 0.015 0.002 TYR A 370 ARG 0.005 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.030 Fit side-chains REVERT: A 85 ARG cc_start: 0.7603 (mtt90) cc_final: 0.6982 (mtm180) REVERT: A 92 LEU cc_start: 0.7489 (mm) cc_final: 0.7227 (mp) REVERT: A 118 GLN cc_start: 0.7935 (tt0) cc_final: 0.7035 (tp-100) REVERT: A 122 ASP cc_start: 0.6107 (m-30) cc_final: 0.5798 (m-30) REVERT: A 216 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 231 GLN cc_start: 0.8170 (mm110) cc_final: 0.7956 (mm-40) REVERT: A 251 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7083 (mt) REVERT: A 808 ASN cc_start: 0.8223 (m-40) cc_final: 0.7363 (m110) REVERT: A 848 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6882 (pp) REVERT: A 859 MET cc_start: 0.6720 (mmt) cc_final: 0.6110 (ptp) REVERT: A 1260 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7882 (tt) REVERT: A 1387 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7091 (mttt) REVERT: A 1389 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7718 (pp) REVERT: A 1651 ARG cc_start: 0.6359 (tpp-160) cc_final: 0.5359 (tmm160) REVERT: A 1692 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7861 (ttm170) outliers start: 31 outliers final: 19 residues processed: 171 average time/residue: 0.2387 time to fit residues: 54.0878 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8735 Z= 0.198 Angle : 0.587 9.716 11806 Z= 0.281 Chirality : 0.042 0.262 1383 Planarity : 0.004 0.062 1414 Dihedral : 12.041 93.005 1589 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 3.10 % Allowed : 17.52 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 992 helix: 1.21 (0.19), residues: 732 sheet: -1.76 (1.59), residues: 12 loop : -1.38 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.020 0.001 PHE A 127 TYR 0.011 0.001 TYR A 374 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.990 Fit side-chains REVERT: A 85 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7060 (mtm180) REVERT: A 92 LEU cc_start: 0.7448 (mm) cc_final: 0.7198 (mp) REVERT: A 122 ASP cc_start: 0.6070 (m-30) cc_final: 0.5794 (m-30) REVERT: A 216 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 251 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6979 (mt) REVERT: A 808 ASN cc_start: 0.8131 (m-40) cc_final: 0.7444 (m110) REVERT: A 848 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6735 (pp) REVERT: A 859 MET cc_start: 0.6682 (mmt) cc_final: 0.6075 (ptp) REVERT: A 1260 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7879 (tt) REVERT: A 1387 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7079 (mttt) REVERT: A 1389 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7726 (pp) REVERT: A 1651 ARG cc_start: 0.6361 (tpp-160) cc_final: 0.5295 (tmm160) REVERT: A 1692 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7863 (ttm170) outliers start: 28 outliers final: 16 residues processed: 165 average time/residue: 0.2297 time to fit residues: 51.3063 Evaluate side-chains 167 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8735 Z= 0.151 Angle : 0.545 10.523 11806 Z= 0.259 Chirality : 0.040 0.255 1383 Planarity : 0.004 0.059 1414 Dihedral : 11.137 90.228 1589 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 3.33 % Allowed : 17.74 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.27), residues: 992 helix: 1.62 (0.20), residues: 733 sheet: -1.46 (1.66), residues: 12 loop : -1.25 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 925 HIS 0.002 0.000 HIS A1609 PHE 0.013 0.001 PHE A 128 TYR 0.009 0.001 TYR A 374 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 0.854 Fit side-chains REVERT: A 85 ARG cc_start: 0.7639 (mtt90) cc_final: 0.6896 (mtm180) REVERT: A 92 LEU cc_start: 0.7390 (mm) cc_final: 0.7186 (mp) REVERT: A 122 ASP cc_start: 0.6051 (m-30) cc_final: 0.5784 (m-30) REVERT: A 216 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 251 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6829 (mt) REVERT: A 808 ASN cc_start: 0.8117 (m-40) cc_final: 0.7320 (m110) REVERT: A 848 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6716 (pp) REVERT: A 859 MET cc_start: 0.6389 (mmt) cc_final: 0.5849 (ptp) REVERT: A 1260 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7881 (tt) REVERT: A 1387 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7007 (mttt) REVERT: A 1389 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7651 (pp) REVERT: A 1651 ARG cc_start: 0.6343 (tpp-160) cc_final: 0.5280 (tmm160) REVERT: A 1692 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7796 (ttm170) outliers start: 30 outliers final: 20 residues processed: 181 average time/residue: 0.2219 time to fit residues: 54.1083 Evaluate side-chains 178 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8735 Z= 0.185 Angle : 0.566 9.848 11806 Z= 0.270 Chirality : 0.041 0.264 1383 Planarity : 0.004 0.060 1414 Dihedral : 11.174 90.687 1587 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 3.33 % Allowed : 17.74 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 992 helix: 1.61 (0.20), residues: 733 sheet: -1.41 (1.68), residues: 12 loop : -1.30 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.020 0.001 PHE A 127 TYR 0.012 0.001 TYR A 374 ARG 0.003 0.000 ARG A 834 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.968 Fit side-chains REVERT: A 85 ARG cc_start: 0.7638 (mtt90) cc_final: 0.6896 (mtm180) REVERT: A 92 LEU cc_start: 0.7443 (mm) cc_final: 0.7171 (mp) REVERT: A 122 ASP cc_start: 0.6135 (m-30) cc_final: 0.5879 (m-30) REVERT: A 216 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 251 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6941 (mt) REVERT: A 808 ASN cc_start: 0.8090 (m-40) cc_final: 0.7266 (m110) REVERT: A 848 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6754 (pp) REVERT: A 859 MET cc_start: 0.6384 (mmt) cc_final: 0.5831 (ttt) REVERT: A 1387 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7019 (mttt) REVERT: A 1389 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 1651 ARG cc_start: 0.6393 (tpp-160) cc_final: 0.5283 (tmm160) REVERT: A 1692 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7792 (ttm170) REVERT: A 1714 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6374 (tpp) outliers start: 30 outliers final: 23 residues processed: 168 average time/residue: 0.2276 time to fit residues: 51.6736 Evaluate side-chains 176 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1714 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8735 Z= 0.193 Angle : 0.572 9.930 11806 Z= 0.274 Chirality : 0.041 0.263 1383 Planarity : 0.004 0.060 1414 Dihedral : 11.195 86.433 1587 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 3.10 % Allowed : 17.85 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 992 helix: 1.63 (0.20), residues: 733 sheet: -1.51 (1.64), residues: 12 loop : -1.33 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.013 0.001 PHE A 868 TYR 0.011 0.001 TYR A 374 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.961 Fit side-chains REVERT: A 85 ARG cc_start: 0.7595 (mtt90) cc_final: 0.6951 (mtm180) REVERT: A 92 LEU cc_start: 0.7447 (mm) cc_final: 0.7181 (mp) REVERT: A 122 ASP cc_start: 0.6074 (m-30) cc_final: 0.5808 (m-30) REVERT: A 216 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 251 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 808 ASN cc_start: 0.8108 (m-40) cc_final: 0.7253 (m110) REVERT: A 848 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6752 (pp) REVERT: A 859 MET cc_start: 0.6352 (mmt) cc_final: 0.5784 (ttt) REVERT: A 1387 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7026 (mttt) REVERT: A 1389 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (pp) REVERT: A 1651 ARG cc_start: 0.6443 (tpp-160) cc_final: 0.5309 (tmm160) REVERT: A 1669 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 1692 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7792 (ttm170) REVERT: A 1714 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6360 (tpp) outliers start: 28 outliers final: 21 residues processed: 166 average time/residue: 0.2341 time to fit residues: 51.8790 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1714 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8735 Z= 0.177 Angle : 0.562 9.673 11806 Z= 0.269 Chirality : 0.041 0.260 1383 Planarity : 0.004 0.059 1414 Dihedral : 11.093 79.078 1587 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 3.10 % Allowed : 17.96 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 992 helix: 1.67 (0.19), residues: 739 sheet: -1.56 (1.62), residues: 12 loop : -1.24 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.020 0.001 PHE A 127 TYR 0.011 0.001 TYR A 374 ARG 0.009 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.955 Fit side-chains REVERT: A 85 ARG cc_start: 0.7285 (mtt90) cc_final: 0.6969 (mtm180) REVERT: A 92 LEU cc_start: 0.7448 (mm) cc_final: 0.7188 (mp) REVERT: A 122 ASP cc_start: 0.6075 (m-30) cc_final: 0.5806 (m-30) REVERT: A 216 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 251 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6915 (mt) REVERT: A 808 ASN cc_start: 0.8091 (m-40) cc_final: 0.7234 (m110) REVERT: A 848 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6794 (pp) REVERT: A 859 MET cc_start: 0.6327 (mmt) cc_final: 0.5771 (ttt) REVERT: A 1387 LYS cc_start: 0.7776 (mtpp) cc_final: 0.7022 (mttt) REVERT: A 1389 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (pp) REVERT: A 1651 ARG cc_start: 0.6420 (tpp-160) cc_final: 0.5311 (tmm160) REVERT: A 1669 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 1692 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7790 (ttm170) REVERT: A 1714 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6428 (tpp) outliers start: 28 outliers final: 21 residues processed: 166 average time/residue: 0.2271 time to fit residues: 50.9450 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1714 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120299 restraints weight = 10442.907| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.80 r_work: 0.2995 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8735 Z= 0.178 Angle : 0.565 9.672 11806 Z= 0.270 Chirality : 0.041 0.261 1383 Planarity : 0.004 0.059 1414 Dihedral : 11.039 77.683 1587 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 2.99 % Allowed : 18.40 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 992 helix: 1.71 (0.20), residues: 739 sheet: -1.60 (1.60), residues: 12 loop : -1.24 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.012 0.001 PHE A 868 TYR 0.011 0.001 TYR A 374 ARG 0.009 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.11 seconds wall clock time: 39 minutes 54.25 seconds (2394.25 seconds total)