Starting phenix.real_space_refine on Tue Nov 14 11:20:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/11_2023/6kzp_0792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/11_2023/6kzp_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_0792/11_2023/6kzp_0792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/11_2023/6kzp_0792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/11_2023/6kzp_0792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/11_2023/6kzp_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 175 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: 5.15, per 1000 atoms: 0.60 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 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: 0.87 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: 2.48 Time building geometry restraints manager: 3.51 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 - 21.82: 4766 21.82 - 43.64: 255 43.64 - 65.45: 55 65.45 - 87.27: 7 87.27 - 109.09: 4 Dihedral angle restraints: 5087 sinusoidal: 2133 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 5084 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: 1.490 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: 0.010 Extract box with map and model: 7.570 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.800 Find NCS groups from input model: 0.240 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.250 ------------------------------------------------------------------------------- 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 : 14.131 109.089 3151 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 *********************** 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 : 0.947 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 240 average time/residue: 0.2389 time to fit residues: 75.4515 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0792 time to fit residues: 2.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 93 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 767 GLN A 805 ASN A 864 ASN A 918 GLN A 957 ASN A1252 HIS A1391 ASN A1442 HIS A1487 ASN 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2811 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= 0.179 Angle : 0.646 9.457 11806 Z= 0.318 Chirality : 0.042 0.281 1383 Planarity : 0.006 0.073 1414 Dihedral : 11.590 110.850 1259 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 2.00 % Allowed : 12.20 % Favored : 85.81 % 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: -2.05 (0.23), residues: 992 helix: -1.01 (0.17), residues: 736 sheet: -3.41 (1.41), residues: 12 loop : -1.83 (0.33), residues: 244 *********************** 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 204 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.014 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 197 average time/residue: 0.2392 time to fit residues: 62.6658 Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1385 time to fit residues: 2.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 83 optimal weight: 0.0870 chunk 92 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 767 GLN A 885 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8735 Z= 0.145 Angle : 0.577 9.540 11806 Z= 0.278 Chirality : 0.042 0.535 1383 Planarity : 0.005 0.064 1414 Dihedral : 10.294 113.230 1259 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 1.88 % Allowed : 14.08 % Favored : 84.04 % 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: -0.41 (0.25), residues: 992 helix: 0.30 (0.19), residues: 738 sheet: -2.98 (1.46), residues: 12 loop : -1.65 (0.34), residues: 242 *********************** 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 188 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 0.945 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 182 average time/residue: 0.2424 time to fit residues: 58.4505 Evaluate side-chains 155 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0884 time to fit residues: 1.9711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8735 Z= 0.177 Angle : 0.574 9.617 11806 Z= 0.276 Chirality : 0.042 0.335 1383 Planarity : 0.005 0.063 1414 Dihedral : 9.719 101.587 1259 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 1.88 % Allowed : 14.30 % Favored : 83.81 % 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: 0.46 (0.26), residues: 992 helix: 0.94 (0.19), residues: 729 sheet: -2.54 (1.45), residues: 12 loop : -1.28 (0.36), residues: 251 *********************** 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 169 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.867 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 161 average time/residue: 0.2376 time to fit residues: 50.6895 Evaluate side-chains 152 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0794 time to fit residues: 2.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3786 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= 0.146 Angle : 0.532 9.572 11806 Z= 0.256 Chirality : 0.041 0.356 1383 Planarity : 0.004 0.063 1414 Dihedral : 9.074 98.047 1259 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 0.89 % Allowed : 16.41 % 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: 1.02 (0.27), residues: 992 helix: 1.37 (0.20), residues: 731 sheet: -2.23 (1.46), residues: 12 loop : -1.19 (0.36), residues: 249 *********************** 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 158 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.851 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 155 average time/residue: 0.2413 time to fit residues: 49.4073 Evaluate side-chains 146 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0784 time to fit residues: 1.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8735 Z= 0.175 Angle : 0.554 9.638 11806 Z= 0.267 Chirality : 0.041 0.321 1383 Planarity : 0.004 0.063 1414 Dihedral : 9.062 96.110 1259 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 16.41 % Favored : 82.26 % 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: 1.23 (0.27), residues: 992 helix: 1.54 (0.20), residues: 733 sheet: -1.88 (1.55), residues: 12 loop : -1.20 (0.37), residues: 247 *********************** 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 161 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.946 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 157 average time/residue: 0.2282 time to fit residues: 48.3466 Evaluate side-chains 149 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0800 time to fit residues: 1.7599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8735 Z= 0.144 Angle : 0.539 9.943 11806 Z= 0.257 Chirality : 0.040 0.278 1383 Planarity : 0.004 0.062 1414 Dihedral : 8.821 93.159 1259 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 0.89 % Allowed : 16.63 % Favored : 82.48 % 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: 1.46 (0.27), residues: 992 helix: 1.72 (0.20), residues: 734 sheet: -1.81 (1.56), residues: 12 loop : -1.19 (0.37), residues: 246 *********************** 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 157 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.974 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 152 average time/residue: 0.2476 time to fit residues: 49.9494 Evaluate side-chains 145 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0798 time to fit residues: 1.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8735 Z= 0.145 Angle : 0.536 9.594 11806 Z= 0.256 Chirality : 0.040 0.267 1383 Planarity : 0.004 0.061 1414 Dihedral : 8.675 90.382 1259 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 0.22 % Allowed : 17.52 % Favored : 82.26 % 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: 1.61 (0.27), residues: 992 helix: 1.85 (0.20), residues: 734 sheet: -1.49 (1.65), residues: 12 loop : -1.19 (0.36), residues: 246 *********************** 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 146 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.984 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.2504 time to fit residues: 48.1069 Evaluate side-chains 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1042 time to fit residues: 1.4767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8735 Z= 0.136 Angle : 0.523 9.578 11806 Z= 0.251 Chirality : 0.039 0.263 1383 Planarity : 0.004 0.061 1414 Dihedral : 8.485 86.475 1259 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 0.22 % Allowed : 17.85 % Favored : 81.93 % 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: 1.77 (0.27), residues: 992 helix: 1.97 (0.20), residues: 734 sheet: -1.48 (1.65), residues: 12 loop : -1.18 (0.36), residues: 246 *********************** 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 146 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.883 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.2505 time to fit residues: 48.3672 Evaluate side-chains 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0804 time to fit residues: 1.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 773 ASN A1782 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8735 Z= 0.267 Angle : 0.627 10.384 11806 Z= 0.301 Chirality : 0.043 0.289 1383 Planarity : 0.004 0.061 1414 Dihedral : 9.364 92.964 1259 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 0.44 % Allowed : 17.96 % 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: 1.26 (0.27), residues: 992 helix: 1.60 (0.19), residues: 731 sheet: -1.67 (1.62), residues: 12 loop : -1.31 (0.37), residues: 249 ********************** 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 148 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.965 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 146 average time/residue: 0.2423 time to fit residues: 47.2224 Evaluate side-chains 147 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0749 time to fit residues: 1.5529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 773 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121051 restraints weight = 10484.504| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.70 r_work: 0.3034 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8735 Z= 0.187 Angle : 0.568 9.677 11806 Z= 0.273 Chirality : 0.041 0.274 1383 Planarity : 0.004 0.061 1414 Dihedral : 9.128 92.193 1259 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 0.22 % Allowed : 18.29 % Favored : 81.49 % 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: 1.47 (0.27), residues: 992 helix: 1.75 (0.20), residues: 732 sheet: -1.55 (1.66), residues: 12 loop : -1.26 (0.37), residues: 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.56 seconds wall clock time: 39 minutes 57.35 seconds (2397.35 seconds total)