Starting phenix.real_space_refine (version: dev) on Thu May 12 22:15:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/05_2022/6kzp_0792_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/05_2022/6kzp_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_0792/05_2022/6kzp_0792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/05_2022/6kzp_0792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/05_2022/6kzp_0792_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzp_0792/05_2022/6kzp_0792_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4597/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: {'DZR': 1, ' CA': 2, 'Y01': 3, 'NAG': 4, '3PE': 8} Classifications: {'undetermined': 18, 'peptide': 1014} 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: 5.52, per 1000 atoms: 0.65 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: 3.62 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 71.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 81 through 99 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) Processing helix chain 'A' and resid 112 through 136 Processing helix chain 'A' and resid 152 through 171 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) Processing helix chain 'A' and resid 180 through 193 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 195 through 233 removed outlier: 3.737A pdb=" N ILE A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Proline residue: A 209 - end of helix removed outlier: 3.842A pdb=" N GLY A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.507A pdb=" N TRP A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.550A pdb=" N PHE A 372 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 373 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 404 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 744 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 770 through 795 removed outlier: 3.546A pdb=" N LEU A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 806 through 822 removed outlier: 4.262A pdb=" N PHE A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 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) removed outlier: 4.209A pdb=" N ARG A 846 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 864 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 866 through 886 removed outlier: 3.532A pdb=" N LEU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.643A pdb=" N THR A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 935 removed outlier: 3.521A pdb=" N ASN A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 removed outlier: 3.717A pdb=" N ALA A 941 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 942 " --> pdb=" O TRP A 939 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 943 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 945 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 947 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 949 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 950 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 951 " --> pdb=" O MET A 948 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A 952 " --> pdb=" O THR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.717A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1251 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 1253 through 1271 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 1284 through 1308 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 1343 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) Processing helix chain 'A' and resid 1350 through 1371 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) removed outlier: 4.370A pdb=" N LEU A1363 " --> pdb=" O LEU A1359 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Proline residue: A1365 - end of helix removed outlier: 5.156A pdb=" N VAL A1368 " --> pdb=" O ARG A1364 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE A1369 " --> pdb=" O PRO A1365 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1411 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) removed outlier: 4.450A pdb=" N LYS A1387 " --> pdb=" O MET A1383 " (cutoff:3.500A) Proline residue: A1388 - end of helix removed outlier: 4.949A pdb=" N ASN A1391 " --> pdb=" O LYS A1387 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE A1392 " --> pdb=" O PRO A1388 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1401 " --> pdb=" O CYS A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1435 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 1449 through 1460 removed outlier: 3.720A pdb=" N MET A1454 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1474 Processing helix chain 'A' and resid 1488 through 1517 removed outlier: 3.588A pdb=" N LEU A1491 " --> pdb=" O PRO A1488 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A1494 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A1495 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A1496 " --> pdb=" O TYR A1493 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A1497 " --> pdb=" O PHE A1494 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A1500 " --> pdb=" O PHE A1497 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A1501 " --> pdb=" O LEU A1498 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A1505 " --> pdb=" O ALA A1502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1506 " --> pdb=" O PHE A1503 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A1509 " --> pdb=" O LEU A1506 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A1510 " --> pdb=" O ASN A1507 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1511 " --> pdb=" O MET A1508 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A1514 " --> pdb=" O GLY A1511 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1515 " --> pdb=" O VAL A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1606 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 1614 through 1642 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 1646 through 1649 No H-bonds generated for 'chain 'A' and resid 1646 through 1649' Processing helix chain 'A' and resid 1652 through 1667 removed outlier: 3.647A pdb=" N ALA A1658 " --> pdb=" O GLN A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1675 Processing helix chain 'A' and resid 1682 through 1699 removed outlier: 4.376A pdb=" N ILE A1693 " --> pdb=" O ARG A1689 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA A1694 " --> pdb=" O VAL A1690 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG A1695 " --> pdb=" O LEU A1691 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL A1696 " --> pdb=" O ARG A1692 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A1697 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A1698 " --> pdb=" O ALA A1694 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU A1699 " --> pdb=" O ARG A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1715 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 1717 through 1742 Processing helix chain 'A' and resid 1765 through 1776 Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1800 through 1835 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) removed outlier: 3.664A pdb=" N GLU A1833 " --> pdb=" O LYS A1829 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 239 through 242 Processing sheet with id= B, first strand: chain 'A' and resid 1416 through 1419 removed outlier: 3.523A pdb=" N ARG A1438 " --> pdb=" O GLN A1419 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1155 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: 2.61 Time building geometry restraints manager: 3.89 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=" C2 NAG A2306 " pdb=" N2 NAG A2306 " pdb=" C7 NAG A2306 " ideal model delta sigma weight residual 123.12 134.13 -11.01 1.28e+00 6.08e-01 7.36e+01 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 ... (remaining 11801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 4786 21.82 - 43.64: 256 43.64 - 65.45: 56 65.45 - 87.27: 8 87.27 - 109.09: 5 Dihedral angle restraints: 5111 sinusoidal: 2157 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=" C3 NAG A2303 " pdb=" C1 NAG A2303 " pdb=" C2 NAG A2303 " pdb=" O5 NAG A2303 " ideal model delta sinusoidal sigma weight residual -50.00 50.00 -100.00 1 2.00e+01 2.50e-03 2.82e+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 ... (remaining 5108 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: 3124 2.89 - 3.39: 8328 3.39 - 3.90: 13112 3.90 - 4.40: 15708 4.40 - 4.90: 25828 Nonbonded interactions: 66100 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 66095 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 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. 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.780 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.110 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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= 0.815 Angle : 1.450 23.926 11806 Z= 0.713 Chirality : 0.077 0.713 1383 Planarity : 0.009 0.102 1414 Dihedral : 14.320 109.089 3175 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 % 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 : 1.048 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 240 average time/residue: 0.2297 time to fit residues: 72.9165 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0772 time to fit residues: 2.8362 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.0670 chunk 93 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 A1487 ASN A1518 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 8735 Z= 0.182 Angle : 0.623 8.329 11806 Z= 0.313 Chirality : 0.041 0.260 1383 Planarity : 0.006 0.087 1414 Dihedral : 12.353 108.958 1283 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer Outliers : 1.77 % 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: -2.13 (0.24), residues: 992 helix: -1.17 (0.17), residues: 718 sheet: -3.38 (1.41), residues: 12 loop : -1.48 (0.34), residues: 262 *********************** 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 200 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.007 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 194 average time/residue: 0.2312 time to fit residues: 60.1644 Evaluate side-chains 163 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0791 time to fit residues: 2.6589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A1487 ASN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1821 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 8735 Z= 0.205 Angle : 0.606 9.203 11806 Z= 0.298 Chirality : 0.043 0.473 1383 Planarity : 0.005 0.058 1414 Dihedral : 11.619 106.862 1283 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 3.10 % 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: -0.66 (0.26), residues: 992 helix: 0.02 (0.19), residues: 705 sheet: -2.96 (1.44), residues: 12 loop : -1.24 (0.35), residues: 275 *********************** 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 181 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.051 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 173 average time/residue: 0.2431 time to fit residues: 56.3193 Evaluate side-chains 160 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1522 time to fit residues: 3.5366 ------------------------------------------------------------------------------- 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: 0.5980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8735 Z= 0.196 Angle : 0.566 6.796 11806 Z= 0.281 Chirality : 0.044 0.577 1383 Planarity : 0.005 0.050 1414 Dihedral : 10.797 103.365 1283 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer Outliers : 1.88 % 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: -0.05 (0.26), residues: 992 helix: 0.53 (0.20), residues: 709 sheet: -2.61 (1.42), residues: 12 loop : -1.21 (0.35), residues: 271 *********************** 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 167 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.081 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 159 average time/residue: 0.2503 time to fit residues: 52.5750 Evaluate side-chains 152 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0829 time to fit residues: 2.8301 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1487 ASN A1782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 8735 Z= 0.206 Angle : 0.560 7.010 11806 Z= 0.279 Chirality : 0.043 0.522 1383 Planarity : 0.005 0.049 1414 Dihedral : 10.535 102.430 1283 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer Outliers : 1.22 % 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: 0.56 (0.27), residues: 992 helix: 0.97 (0.20), residues: 693 sheet: -2.46 (1.38), residues: 12 loop : -0.84 (0.36), residues: 287 *********************** 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: 11 poor density : 147 time to evaluate : 1.016 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 153 average time/residue: 0.2381 time to fit residues: 48.8749 Evaluate side-chains 147 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0796 time to fit residues: 2.0128 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 58 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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: 0.8096 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 8735 Z= 0.165 Angle : 0.525 7.375 11806 Z= 0.263 Chirality : 0.041 0.513 1383 Planarity : 0.004 0.049 1414 Dihedral : 10.086 102.282 1283 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.58 % Rotamer Outliers : 0.55 % 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: 0.97 (0.27), residues: 992 helix: 1.27 (0.20), residues: 696 sheet: -2.21 (1.45), residues: 12 loop : -0.68 (0.37), residues: 284 *********************** 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 156 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.018 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 154 average time/residue: 0.2373 time to fit residues: 49.2544 Evaluate side-chains 146 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0969 time to fit residues: 1.8903 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 918 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 8735 Z= 0.192 Angle : 0.550 8.029 11806 Z= 0.274 Chirality : 0.042 0.513 1383 Planarity : 0.004 0.049 1414 Dihedral : 10.099 102.200 1283 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer Outliers : 1.11 % 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: 1.01 (0.27), residues: 992 helix: 1.30 (0.20), residues: 697 sheet: -1.94 (1.54), residues: 12 loop : -0.70 (0.37), residues: 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 155 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.072 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.2342 time to fit residues: 47.3503 Evaluate side-chains 147 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0832 time to fit residues: 2.2792 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8095 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 8735 Z= 0.165 Angle : 0.537 10.165 11806 Z= 0.266 Chirality : 0.041 0.506 1383 Planarity : 0.004 0.048 1414 Dihedral : 9.903 102.370 1283 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.44 % 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: 1.10 (0.28), residues: 992 helix: 1.34 (0.20), residues: 712 sheet: -1.66 (1.62), residues: 12 loop : -0.71 (0.37), residues: 268 *********************** 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 151 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.052 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 148 average time/residue: 0.2327 time to fit residues: 46.6798 Evaluate side-chains 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0830 time to fit residues: 1.6884 ------------------------------------------------------------------------------- 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: 0.8980 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 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: 0.8109 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 8735 Z= 0.191 Angle : 0.554 9.859 11806 Z= 0.274 Chirality : 0.042 0.505 1383 Planarity : 0.004 0.048 1414 Dihedral : 9.981 102.138 1283 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer Outliers : 0.11 % 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: 1.06 (0.27), residues: 992 helix: 1.31 (0.20), residues: 711 sheet: -1.58 (1.64), residues: 12 loop : -0.73 (0.37), residues: 269 *********************** 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 140 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.065 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.2448 time to fit residues: 46.1727 Evaluate side-chains 140 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0788 time to fit residues: 1.5350 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 8735 Z= 0.165 Angle : 0.531 9.293 11806 Z= 0.264 Chirality : 0.041 0.504 1383 Planarity : 0.004 0.048 1414 Dihedral : 9.828 102.293 1283 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.11 % 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: 1.25 (0.28), residues: 992 helix: 1.45 (0.20), residues: 711 sheet: -1.71 (1.60), residues: 12 loop : -0.64 (0.38), residues: 269 ********************** 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: 1 poor density : 147 time to evaluate : 1.012 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.2283 time to fit residues: 45.8759 Evaluate side-chains 141 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0780 time to fit residues: 1.5338 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.155649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121328 restraints weight = 10455.852| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.66 r_work: 0.3175 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.3138 rms_B_bonded: 1.59 restraints_weight: 0.1250 r_work: 0.3116 rms_B_bonded: 1.80 restraints_weight: 0.0625 r_work: 0.3089 rms_B_bonded: 2.12 restraints_weight: 0.0312 r_work: 0.3056 rms_B_bonded: 2.56 restraints_weight: 0.0156 r_work: 0.3015 rms_B_bonded: 3.19 restraints_weight: 0.0078 r_work: 0.2961 rms_B_bonded: 4.07 restraints_weight: 0.0039 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 8735 Z= 0.157 Angle : 0.531 9.139 11806 Z= 0.263 Chirality : 0.041 0.500 1383 Planarity : 0.004 0.048 1414 Dihedral : 9.709 102.322 1283 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.11 % 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: 1.34 (0.28), residues: 992 helix: 1.54 (0.20), residues: 709 sheet: -1.53 (1.65), residues: 12 loop : -0.67 (0.38), residues: 271 =============================================================================== Job complete usr+sys time: 1900.31 seconds wall clock time: 35 minutes 5.90 seconds (2105.90 seconds total)