Starting phenix.real_space_refine on Fri Mar 15 00:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtd_30851/03_2024/7dtd_30851_updated.pdb" } resolution = 3.3 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= 0.001 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6739 2.51 5 N 1596 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 823": "OD1" <-> "OD2" Residue "A TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 926": "OD1" <-> "OD2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1256": "OD1" <-> "OD2" Residue "A TYR 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1288": "OD1" <-> "OD2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A ARG 1322": "NH1" <-> "NH2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A TYR 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1383": "OD1" <-> "OD2" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1386": "OD1" <-> "OD2" Residue "A ASP 1395": "OD1" <-> "OD2" Residue "A GLU 1404": "OE1" <-> "OE2" Residue "A ASP 1436": "OD1" <-> "OD2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A GLU 1455": "OE1" <-> "OE2" Residue "A TYR 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1561": "OE1" <-> "OE2" Residue "A ASP 1564": "OD1" <-> "OD2" Residue "A TYR 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1639": "NH1" <-> "NH2" Residue "A ARG 1642": "NH1" <-> "NH2" Residue "A PHE 1682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1727": "OD1" <-> "OD2" Residue "A PHE 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1765": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10190 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 111, 881 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 111, 881 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 871 Chain: "A" Number of atoms: 9287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1143, 9287 Unusual residues: {'9Z9': 1, 'NAG': 4} Classifications: {'peptide': 1138, 'undetermined': 5} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1108, None: 5} Not linked: pdbres="GLU A1795 " pdbres="NAG A2101 " Not linked: pdbres="NAG A2101 " pdbres="NAG A2102 " Not linked: pdbres="NAG A2102 " pdbres="NAG A2103 " Not linked: pdbres="NAG A2103 " pdbres="NAG A2104 " Not linked: pdbres="NAG A2104 " pdbres="9Z9 A2105 " Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.97, per 1000 atoms: 0.59 Number of scatterers: 10190 At special positions: 0 Unit cell: (137.238, 139.433, 104.301, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1777 8.00 N 1596 7.00 C 6739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 131 " distance=2.10 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS A 919 " distance=2.08 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 345 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 351 " distance=2.01 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A 927 " distance=2.03 Simple disulfide: pdb=" SG CYS A 959 " - pdb=" SG CYS A 968 " distance=2.04 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1396 " distance=2.03 Simple disulfide: pdb=" SG CYS A1741 " - pdb=" SG CYS A1756 " distance=2.03 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 A2101 " - " ASN A1403 " " NAG A2102 " - " ASN A1392 " " NAG A2103 " - " ASN A1378 " " NAG A2104 " - " ASN A 338 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 62.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'A' and resid 117 through 125 removed outlier: 4.094A pdb=" N ALA A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 145 Processing helix chain 'A' and resid 152 through 176 removed outlier: 3.911A pdb=" N ASN A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 234 through 268 removed outlier: 4.165A pdb=" N LYS A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 397 through 438 removed outlier: 3.943A pdb=" N ILE A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 407 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A 411 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 413 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU A 414 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 415 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 427 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 428 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 4.246A pdb=" N VAL A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 removed outlier: 3.740A pdb=" N THR A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 821 removed outlier: 4.638A pdb=" N VAL A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 820 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 847 Processing helix chain 'A' and resid 856 through 871 removed outlier: 4.291A pdb=" N ARG A 862 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 864 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 865 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 887 removed outlier: 4.379A pdb=" N VAL A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 911 Processing helix chain 'A' and resid 915 through 918 No H-bonds generated for 'chain 'A' and resid 915 through 918' Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 937 through 949 Processing helix chain 'A' and resid 954 through 963 removed outlier: 4.005A pdb=" N ASP A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 994 removed outlier: 4.175A pdb=" N ASN A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1215 Processing helix chain 'A' and resid 1218 through 1235 removed outlier: 3.612A pdb=" N THR A1222 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1244 removed outlier: 3.905A pdb=" N ASP A1243 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1274 removed outlier: 3.596A pdb=" N LYS A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A1267 " --> pdb=" O PHE A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1280 Processing helix chain 'A' and resid 1283 through 1304 Processing helix chain 'A' and resid 1312 through 1326 removed outlier: 4.581A pdb=" N THR A1317 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A1320 " --> pdb=" O ARG A1316 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG A1322 " --> pdb=" O LEU A1318 " (cutoff:3.500A) Proline residue: A1323 - end of helix removed outlier: 5.023A pdb=" N ALA A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1341 removed outlier: 3.719A pdb=" N VAL A1336 " --> pdb=" O GLY A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1368 removed outlier: 3.884A pdb=" N VAL A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A1361 " --> pdb=" O PHE A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1402 Processing helix chain 'A' and resid 1418 through 1430 Processing helix chain 'A' and resid 1434 through 1442 Processing helix chain 'A' and resid 1457 through 1493 removed outlier: 3.583A pdb=" N TYR A1460 " --> pdb=" O LEU A1457 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY A1470 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1471 " --> pdb=" O ILE A1468 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A1472 " --> pdb=" O PHE A1469 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE A1473 " --> pdb=" O GLY A1470 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR A1474 " --> pdb=" O SER A1471 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A1493 " --> pdb=" O LYS A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1514 removed outlier: 3.537A pdb=" N MET A1511 " --> pdb=" O TYR A1507 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A1513 " --> pdb=" O ASN A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1538 Processing helix chain 'A' and resid 1541 through 1559 Processing helix chain 'A' and resid 1567 through 1594 removed outlier: 3.662A pdb=" N ILE A1593 " --> pdb=" O VAL A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1620 Processing helix chain 'A' and resid 1632 through 1651 removed outlier: 3.836A pdb=" N LEU A1640 " --> pdb=" O ARG A1636 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A1641 " --> pdb=" O VAL A1637 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG A1642 " --> pdb=" O ILE A1638 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A1644 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A1645 " --> pdb=" O ALA A1641 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A1646 " --> pdb=" O ARG A1642 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A1648 " --> pdb=" O GLY A1644 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A1649 " --> pdb=" O ARG A1645 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE A1650 " --> pdb=" O ILE A1646 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS A1651 " --> pdb=" O LEU A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1691 Proline residue: A1668 - end of helix removed outlier: 4.049A pdb=" N ASN A1672 " --> pdb=" O PRO A1668 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1722 removed outlier: 3.522A pdb=" N GLN A1719 " --> pdb=" O ILE A1715 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A1722 " --> pdb=" O PHE A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1733 Proline residue: A1732 - end of helix Processing helix chain 'A' and resid 1759 through 1792 removed outlier: 4.022A pdb=" N GLU A1787 " --> pdb=" O ALA A1783 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1790 " --> pdb=" O LEU A1786 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 40 through 44 removed outlier: 6.303A pdb=" N PHE B 148 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA B 43 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN B 150 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 80 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 70 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 78 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR B 83 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B 93 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 132 through 135 Processing sheet with id= D, first strand: chain 'A' and resid 1375 through 1378 550 hydrogen bonds defined for protein. 1373 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: 3.00 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3072 1.35 - 1.47: 2763 1.47 - 1.60: 4484 1.60 - 1.72: 0 1.72 - 1.85: 127 Bond restraints: 10446 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CA GLU A 853 " pdb=" C GLU A 853 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.34e-02 5.57e+03 2.46e+00 bond pdb=" CA LYS B 77 " pdb=" C LYS B 77 " ideal model delta sigma weight residual 1.520 1.502 0.019 1.22e-02 6.72e+03 2.40e+00 bond pdb=" C04 9Z9 A2105 " pdb=" O72 9Z9 A2105 " ideal model delta sigma weight residual 1.420 1.389 0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CA LEU B 149 " pdb=" C LEU B 149 " ideal model delta sigma weight residual 1.523 1.505 0.019 1.24e-02 6.50e+03 2.29e+00 ... (remaining 10441 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.35: 229 106.35 - 113.30: 5695 113.30 - 120.26: 4045 120.26 - 127.21: 4118 127.21 - 134.16: 91 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N ARG A 322 " pdb=" CA ARG A 322 " pdb=" C ARG A 322 " ideal model delta sigma weight residual 114.31 107.98 6.33 1.29e+00 6.01e-01 2.40e+01 angle pdb=" N TYR A 826 " pdb=" CA TYR A 826 " pdb=" C TYR A 826 " ideal model delta sigma weight residual 113.02 107.43 5.59 1.20e+00 6.94e-01 2.17e+01 angle pdb=" N VAL A 765 " pdb=" CA VAL A 765 " pdb=" C VAL A 765 " ideal model delta sigma weight residual 106.21 111.13 -4.92 1.07e+00 8.73e-01 2.12e+01 angle pdb=" N HIS A1597 " pdb=" CA HIS A1597 " pdb=" C HIS A1597 " ideal model delta sigma weight residual 114.62 109.40 5.22 1.14e+00 7.69e-01 2.10e+01 angle pdb=" C GLY A 854 " pdb=" N LEU A 855 " pdb=" CA LEU A 855 " ideal model delta sigma weight residual 122.95 115.38 7.57 1.66e+00 3.63e-01 2.08e+01 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 5770 22.99 - 45.99: 415 45.99 - 68.98: 54 68.98 - 91.97: 7 91.97 - 114.97: 1 Dihedral angle restraints: 6247 sinusoidal: 2581 harmonic: 3666 Sorted by residual: dihedral pdb=" CA ARG A1525 " pdb=" C ARG A1525 " pdb=" N PRO A1526 " pdb=" CA PRO A1526 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL A 765 " pdb=" C VAL A 765 " pdb=" N MET A 766 " pdb=" CA MET A 766 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 186 " pdb=" C LEU A 186 " pdb=" N ARG A 187 " pdb=" CA ARG A 187 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 6244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1259 0.051 - 0.103: 324 0.103 - 0.154: 48 0.154 - 0.206: 11 0.206 - 0.257: 7 Chirality restraints: 1649 Sorted by residual: chirality pdb=" CA AASP B 97 " pdb=" N ASP B 97 " pdb=" C ASP B 97 " pdb=" CB AASP B 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU A 186 " pdb=" CB LEU A 186 " pdb=" CD1 LEU A 186 " pdb=" CD2 LEU A 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL B 84 " pdb=" N VAL B 84 " pdb=" C VAL B 84 " pdb=" CB VAL B 84 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1646 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 852 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C VAL A 852 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 852 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 853 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1434 " -0.013 2.00e-02 2.50e+03 1.51e-02 5.70e+00 pdb=" CG TRP A1434 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A1434 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1434 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1434 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1434 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1434 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1434 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1434 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1434 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 357 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO A 358 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.031 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 179 2.67 - 3.22: 10386 3.22 - 3.78: 15230 3.78 - 4.34: 20871 4.34 - 4.90: 33401 Nonbonded interactions: 80067 Sorted by model distance: nonbonded pdb=" O ILE A 318 " pdb=" CG GLN A 319 " model vdw 2.107 3.440 nonbonded pdb=" O THR A 793 " pdb=" N PHE A 796 " model vdw 2.279 2.520 nonbonded pdb=" OD1 ASN A1410 " pdb=" N VAL A1411 " model vdw 2.291 2.520 nonbonded pdb=" O THR A 793 " pdb=" N HIS A 795 " model vdw 2.334 2.520 nonbonded pdb=" O SER A 856 " pdb=" OG SER A 856 " model vdw 2.341 2.440 ... (remaining 80062 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=0.26 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: 0.510 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: 2.350 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.280 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.004 0.043 10446 Z= 0.269 Angle : 0.845 9.753 14178 Z= 0.537 Chirality : 0.049 0.257 1649 Planarity : 0.004 0.057 1727 Dihedral : 15.192 114.968 3855 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.76 % Favored : 91.35 % Rotamer: Outliers : 2.23 % Allowed : 7.06 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.18 (0.21), residues: 1242 helix: -1.36 (0.16), residues: 765 sheet: -1.22 (0.56), residues: 75 loop : -3.64 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1434 HIS 0.007 0.001 HIS B 144 PHE 0.015 0.001 PHE A 383 TYR 0.020 0.001 TYR A 388 ARG 0.003 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8143 (ttp) cc_final: 0.7909 (ttm) REVERT: A 409 LEU cc_start: 0.8754 (mm) cc_final: 0.8447 (mm) REVERT: A 424 MET cc_start: 0.8268 (tpt) cc_final: 0.7466 (mtm) REVERT: A 815 MET cc_start: 0.8228 (tpp) cc_final: 0.8005 (tpp) REVERT: A 839 ILE cc_start: 0.8471 (mm) cc_final: 0.8263 (mm) REVERT: A 853 GLU cc_start: 0.0716 (OUTLIER) cc_final: 0.0280 (tm-30) REVERT: A 1214 ILE cc_start: 0.8713 (mm) cc_final: 0.8496 (mm) REVERT: A 1219 TRP cc_start: 0.7457 (m-10) cc_final: 0.6982 (m-90) REVERT: A 1226 PHE cc_start: 0.8248 (t80) cc_final: 0.7956 (t80) REVERT: A 1267 MET cc_start: 0.8252 (ttp) cc_final: 0.7622 (tmm) REVERT: A 1277 GLN cc_start: 0.8293 (tp40) cc_final: 0.7265 (mt0) REVERT: A 1608 ASP cc_start: 0.7872 (t70) cc_final: 0.7463 (t70) REVERT: A 1665 MET cc_start: 0.6995 (mmt) cc_final: 0.6412 (mmt) outliers start: 25 outliers final: 12 residues processed: 253 average time/residue: 0.2197 time to fit residues: 79.7662 Evaluate side-chains 180 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1751 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0020 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 272 ASN A 275 ASN A 319 GLN A 381 GLN A 429 GLN A 933 HIS A 980 ASN A1217 HIS A1367 ASN A1375 HIS A1554 ASN A1735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10446 Z= 0.188 Angle : 0.654 10.557 14178 Z= 0.339 Chirality : 0.041 0.168 1649 Planarity : 0.005 0.043 1727 Dihedral : 7.933 67.306 1544 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.92 % Favored : 91.84 % Rotamer: Outliers : 2.68 % Allowed : 13.32 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.43 (0.24), residues: 1242 helix: -0.00 (0.19), residues: 759 sheet: -0.91 (0.54), residues: 87 loop : -2.76 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1434 HIS 0.003 0.001 HIS A1393 PHE 0.018 0.001 PHE A 256 TYR 0.021 0.002 TYR A 825 ARG 0.005 0.000 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8516 (tpt) cc_final: 0.7675 (mtm) REVERT: A 766 MET cc_start: 0.6214 (tpt) cc_final: 0.5892 (tpt) REVERT: A 787 MET cc_start: 0.8184 (mtp) cc_final: 0.7922 (mtp) REVERT: A 816 PHE cc_start: 0.7139 (m-80) cc_final: 0.6898 (m-80) REVERT: A 841 THR cc_start: 0.8871 (p) cc_final: 0.8639 (t) REVERT: A 918 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7131 (t0) REVERT: A 1214 ILE cc_start: 0.8686 (mm) cc_final: 0.8473 (mm) REVERT: A 1219 TRP cc_start: 0.7525 (m-10) cc_final: 0.7055 (m-90) REVERT: A 1226 PHE cc_start: 0.8170 (t80) cc_final: 0.7834 (t80) REVERT: A 1266 GLU cc_start: 0.8034 (pp20) cc_final: 0.7647 (pp20) REVERT: A 1277 GLN cc_start: 0.8303 (tp40) cc_final: 0.7243 (mt0) REVERT: A 1313 LYS cc_start: 0.8305 (tmtt) cc_final: 0.8020 (tmtt) REVERT: A 1548 MET cc_start: 0.7336 (mtt) cc_final: 0.6996 (tpp) REVERT: A 1608 ASP cc_start: 0.7906 (t70) cc_final: 0.7603 (t70) outliers start: 30 outliers final: 20 residues processed: 198 average time/residue: 0.1903 time to fit residues: 55.0262 Evaluate side-chains 182 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 416 ASN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10446 Z= 0.183 Angle : 0.598 8.988 14178 Z= 0.312 Chirality : 0.040 0.165 1649 Planarity : 0.004 0.039 1727 Dihedral : 7.014 63.879 1533 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 3.75 % Allowed : 16.35 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.90 (0.24), residues: 1242 helix: 0.32 (0.19), residues: 759 sheet: -0.48 (0.55), residues: 85 loop : -2.37 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1434 HIS 0.003 0.001 HIS A1393 PHE 0.018 0.001 PHE A1466 TYR 0.020 0.002 TYR A 388 ARG 0.005 0.000 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8350 (tpt) cc_final: 0.7524 (mtm) REVERT: A 766 MET cc_start: 0.6389 (tpt) cc_final: 0.6130 (tpt) REVERT: A 918 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7213 (t0) REVERT: A 1214 ILE cc_start: 0.8681 (mm) cc_final: 0.8435 (mm) REVERT: A 1219 TRP cc_start: 0.7548 (m-10) cc_final: 0.7050 (m-90) REVERT: A 1266 GLU cc_start: 0.8069 (pp20) cc_final: 0.7741 (pp20) REVERT: A 1277 GLN cc_start: 0.8283 (tp40) cc_final: 0.7189 (mt0) REVERT: A 1348 MET cc_start: 0.6812 (tpp) cc_final: 0.6586 (mmt) REVERT: A 1500 MET cc_start: 0.6841 (mtt) cc_final: 0.6610 (mtp) REVERT: A 1548 MET cc_start: 0.7419 (mtt) cc_final: 0.7069 (tpp) REVERT: A 1608 ASP cc_start: 0.7887 (t70) cc_final: 0.7567 (t70) outliers start: 41 outliers final: 27 residues processed: 199 average time/residue: 0.1866 time to fit residues: 54.8644 Evaluate side-chains 189 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN A1577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10446 Z= 0.414 Angle : 0.724 9.973 14178 Z= 0.373 Chirality : 0.046 0.221 1649 Planarity : 0.005 0.046 1727 Dihedral : 7.432 59.812 1531 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.46 % Favored : 90.22 % Rotamer: Outliers : 5.27 % Allowed : 17.34 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.24 (0.24), residues: 1242 helix: 0.02 (0.18), residues: 767 sheet: -0.49 (0.57), residues: 85 loop : -2.51 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1434 HIS 0.007 0.001 HIS A1393 PHE 0.025 0.002 PHE A 200 TYR 0.033 0.002 TYR A 388 ARG 0.004 0.001 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 160 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8460 (tt) cc_final: 0.7914 (tp) REVERT: A 370 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.8240 (m100) REVERT: A 424 MET cc_start: 0.8339 (tpt) cc_final: 0.7524 (mtm) REVERT: A 792 MET cc_start: 0.7767 (mmm) cc_final: 0.6820 (mtt) REVERT: A 841 THR cc_start: 0.8843 (p) cc_final: 0.8625 (t) REVERT: A 918 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7428 (t0) REVERT: A 1214 ILE cc_start: 0.8705 (mm) cc_final: 0.8451 (mm) REVERT: A 1219 TRP cc_start: 0.7559 (m-10) cc_final: 0.7043 (m-90) REVERT: A 1267 MET cc_start: 0.8164 (tmm) cc_final: 0.7751 (tmm) REVERT: A 1277 GLN cc_start: 0.8356 (tp40) cc_final: 0.7199 (mt0) REVERT: A 1548 MET cc_start: 0.7313 (mtt) cc_final: 0.7049 (tpp) REVERT: A 1608 ASP cc_start: 0.7844 (t70) cc_final: 0.7393 (t70) outliers start: 58 outliers final: 37 residues processed: 200 average time/residue: 0.1905 time to fit residues: 56.9027 Evaluate side-chains 192 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10446 Z= 0.250 Angle : 0.657 12.575 14178 Z= 0.336 Chirality : 0.042 0.189 1649 Planarity : 0.004 0.041 1727 Dihedral : 7.003 59.718 1529 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.75 % Rotamer: Outliers : 4.74 % Allowed : 19.48 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.98 (0.24), residues: 1242 helix: 0.22 (0.19), residues: 774 sheet: -0.39 (0.58), residues: 87 loop : -2.45 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1434 HIS 0.004 0.001 HIS A1393 PHE 0.024 0.001 PHE A 200 TYR 0.023 0.002 TYR A 388 ARG 0.003 0.000 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 PHE cc_start: 0.7706 (t80) cc_final: 0.7463 (t80) REVERT: A 278 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 424 MET cc_start: 0.8336 (tpt) cc_final: 0.7622 (mtm) REVERT: A 766 MET cc_start: 0.6537 (tpt) cc_final: 0.6195 (tpt) REVERT: A 792 MET cc_start: 0.7857 (mmm) cc_final: 0.6813 (mtt) REVERT: A 794 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7290 (t0) REVERT: A 822 MET cc_start: 0.7209 (pmm) cc_final: 0.6916 (ptm) REVERT: A 841 THR cc_start: 0.8760 (p) cc_final: 0.8558 (t) REVERT: A 1214 ILE cc_start: 0.8707 (mm) cc_final: 0.8444 (mm) REVERT: A 1219 TRP cc_start: 0.7540 (m-10) cc_final: 0.6994 (m-90) REVERT: A 1267 MET cc_start: 0.8184 (tmm) cc_final: 0.7736 (tmm) REVERT: A 1277 GLN cc_start: 0.8296 (tp40) cc_final: 0.7169 (mt0) REVERT: A 1500 MET cc_start: 0.6741 (mtt) cc_final: 0.6533 (mtp) REVERT: A 1608 ASP cc_start: 0.7780 (t70) cc_final: 0.7325 (t70) outliers start: 52 outliers final: 32 residues processed: 199 average time/residue: 0.1973 time to fit residues: 59.6070 Evaluate side-chains 186 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 10446 Z= 0.364 Angle : 0.730 13.899 14178 Z= 0.372 Chirality : 0.045 0.216 1649 Planarity : 0.005 0.040 1727 Dihedral : 7.006 59.051 1525 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.62 % Favored : 90.14 % Rotamer: Outliers : 5.36 % Allowed : 19.48 % Favored : 75.16 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.12 % 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: -1.11 (0.24), residues: 1242 helix: 0.13 (0.18), residues: 770 sheet: -0.52 (0.57), residues: 85 loop : -2.50 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1434 HIS 0.007 0.001 HIS A1393 PHE 0.026 0.002 PHE A 200 TYR 0.029 0.002 TYR A 388 ARG 0.003 0.000 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.8242 (m100) REVERT: A 424 MET cc_start: 0.8345 (tpt) cc_final: 0.7584 (mtm) REVERT: A 766 MET cc_start: 0.6606 (tpt) cc_final: 0.6279 (tpt) REVERT: A 792 MET cc_start: 0.7753 (mmm) cc_final: 0.6795 (mtt) REVERT: A 794 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7299 (t0) REVERT: A 800 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8257 (mm) REVERT: A 822 MET cc_start: 0.7492 (pmm) cc_final: 0.6822 (ptm) REVERT: A 841 THR cc_start: 0.8790 (p) cc_final: 0.8563 (t) REVERT: A 976 MET cc_start: 0.8533 (ttp) cc_final: 0.8256 (mtp) REVERT: A 1214 ILE cc_start: 0.8718 (mm) cc_final: 0.8457 (mm) REVERT: A 1219 TRP cc_start: 0.7509 (m-10) cc_final: 0.6990 (m-90) REVERT: A 1267 MET cc_start: 0.8140 (tmm) cc_final: 0.7691 (tmm) REVERT: A 1277 GLN cc_start: 0.8322 (tp40) cc_final: 0.8060 (tp40) REVERT: A 1475 LEU cc_start: 0.8580 (tp) cc_final: 0.8342 (tp) REVERT: A 1608 ASP cc_start: 0.7816 (t70) cc_final: 0.7324 (t70) outliers start: 59 outliers final: 42 residues processed: 196 average time/residue: 0.1807 time to fit residues: 53.0509 Evaluate side-chains 201 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 191 ASN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10446 Z= 0.198 Angle : 0.636 13.741 14178 Z= 0.325 Chirality : 0.041 0.179 1649 Planarity : 0.004 0.042 1727 Dihedral : 6.495 58.179 1525 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.67 % Rotamer: Outliers : 4.38 % Allowed : 20.73 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.75 (0.24), residues: 1242 helix: 0.45 (0.19), residues: 764 sheet: 0.28 (0.60), residues: 73 loop : -2.49 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1408 HIS 0.003 0.001 HIS A1393 PHE 0.027 0.001 PHE A 200 TYR 0.019 0.001 TYR A 388 ARG 0.002 0.000 ARG A1639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8261 (tpt) cc_final: 0.7568 (mtm) REVERT: A 766 MET cc_start: 0.6382 (tpt) cc_final: 0.6099 (tpt) REVERT: A 800 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 841 THR cc_start: 0.8727 (p) cc_final: 0.8523 (t) REVERT: A 1214 ILE cc_start: 0.8691 (mm) cc_final: 0.8423 (mm) REVERT: A 1219 TRP cc_start: 0.7534 (m-10) cc_final: 0.6987 (m-90) REVERT: A 1267 MET cc_start: 0.8070 (tmm) cc_final: 0.7552 (tmm) REVERT: A 1277 GLN cc_start: 0.8271 (tp40) cc_final: 0.7988 (tp40) REVERT: A 1475 LEU cc_start: 0.8584 (tp) cc_final: 0.8382 (tp) REVERT: A 1608 ASP cc_start: 0.7735 (t70) cc_final: 0.7285 (t70) outliers start: 48 outliers final: 33 residues processed: 197 average time/residue: 0.1771 time to fit residues: 52.4386 Evaluate side-chains 191 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10446 Z= 0.435 Angle : 0.755 14.491 14178 Z= 0.387 Chirality : 0.047 0.225 1649 Planarity : 0.005 0.039 1727 Dihedral : 6.830 59.818 1522 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.05 % Favored : 90.62 % Rotamer: Outliers : 5.36 % Allowed : 19.66 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.15 (0.24), residues: 1242 helix: 0.11 (0.18), residues: 775 sheet: -0.48 (0.56), residues: 87 loop : -2.58 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 754 HIS 0.010 0.001 HIS A 759 PHE 0.022 0.002 PHE A 256 TYR 0.034 0.002 TYR A 388 ARG 0.003 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 156 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8426 (tt) cc_final: 0.7938 (tp) REVERT: A 370 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.8254 (m100) REVERT: A 424 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: A 766 MET cc_start: 0.6691 (tpt) cc_final: 0.6402 (tpt) REVERT: A 841 THR cc_start: 0.8812 (p) cc_final: 0.8585 (t) REVERT: A 918 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7273 (t70) REVERT: A 1214 ILE cc_start: 0.8725 (mm) cc_final: 0.8465 (mm) REVERT: A 1219 TRP cc_start: 0.7532 (m-10) cc_final: 0.6988 (m-90) REVERT: A 1277 GLN cc_start: 0.8312 (tp40) cc_final: 0.8002 (tp40) REVERT: A 1475 LEU cc_start: 0.8619 (tp) cc_final: 0.8400 (tp) REVERT: A 1608 ASP cc_start: 0.7788 (t70) cc_final: 0.7291 (t70) outliers start: 59 outliers final: 43 residues processed: 196 average time/residue: 0.1809 time to fit residues: 53.5887 Evaluate side-chains 194 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1760 SER Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.2980 chunk 115 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 118 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: B 140 ASN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10446 Z= 0.167 Angle : 0.636 15.532 14178 Z= 0.323 Chirality : 0.041 0.186 1649 Planarity : 0.004 0.042 1727 Dihedral : 6.194 57.581 1522 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.67 % Rotamer: Outliers : 3.49 % Allowed : 22.25 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.71 (0.24), residues: 1242 helix: 0.47 (0.19), residues: 774 sheet: -0.26 (0.56), residues: 91 loop : -2.47 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1408 HIS 0.008 0.001 HIS A 759 PHE 0.023 0.001 PHE A 256 TYR 0.016 0.001 TYR A 388 ARG 0.006 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8255 (mmt) cc_final: 0.7853 (mmm) REVERT: A 278 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 424 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7551 (mtm) REVERT: A 766 MET cc_start: 0.6577 (tpt) cc_final: 0.6332 (tpt) REVERT: A 841 THR cc_start: 0.8754 (p) cc_final: 0.8537 (t) REVERT: A 918 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6959 (t70) REVERT: A 1214 ILE cc_start: 0.8685 (mm) cc_final: 0.8411 (mm) REVERT: A 1219 TRP cc_start: 0.7529 (m-10) cc_final: 0.6974 (m-90) REVERT: A 1277 GLN cc_start: 0.8256 (tp40) cc_final: 0.7939 (tp40) REVERT: A 1435 MET cc_start: 0.7949 (mmp) cc_final: 0.7728 (mmp) REVERT: A 1608 ASP cc_start: 0.7736 (t70) cc_final: 0.7295 (t70) outliers start: 38 outliers final: 26 residues processed: 181 average time/residue: 0.1824 time to fit residues: 49.9567 Evaluate side-chains 184 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10446 Z= 0.348 Angle : 0.718 15.601 14178 Z= 0.366 Chirality : 0.045 0.213 1649 Planarity : 0.005 0.039 1727 Dihedral : 6.550 58.883 1522 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.33 % Favored : 91.43 % Rotamer: Outliers : 4.02 % Allowed : 22.43 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.86 (0.24), residues: 1242 helix: 0.27 (0.18), residues: 770 sheet: -0.21 (0.57), residues: 91 loop : -2.33 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 754 HIS 0.007 0.001 HIS A1393 PHE 0.022 0.002 PHE A1774 TYR 0.032 0.002 TYR A 388 ARG 0.007 0.000 ARG A 862 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8203 (mmt) cc_final: 0.8002 (mmt) REVERT: A 370 TRP cc_start: 0.8456 (OUTLIER) cc_final: 0.8128 (m100) REVERT: A 424 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7620 (mtm) REVERT: A 766 MET cc_start: 0.6737 (tpt) cc_final: 0.6480 (tpt) REVERT: A 841 THR cc_start: 0.8771 (p) cc_final: 0.8534 (t) REVERT: A 862 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.7272 (ptm-80) REVERT: A 918 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7121 (t70) REVERT: A 1214 ILE cc_start: 0.8713 (mm) cc_final: 0.8450 (mm) REVERT: A 1219 TRP cc_start: 0.7580 (m-10) cc_final: 0.6992 (m-90) REVERT: A 1277 GLN cc_start: 0.8295 (tp40) cc_final: 0.7985 (tp40) REVERT: A 1608 ASP cc_start: 0.7836 (t70) cc_final: 0.7358 (t70) outliers start: 44 outliers final: 33 residues processed: 185 average time/residue: 0.1711 time to fit residues: 47.8034 Evaluate side-chains 186 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1239 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1740 ASP Chi-restraints excluded: chain A residue 1760 SER Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.162647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125429 restraints weight = 46460.984| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.25 r_work: 0.3442 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10446 Z= 0.210 Angle : 0.660 15.988 14178 Z= 0.333 Chirality : 0.043 0.229 1649 Planarity : 0.004 0.041 1727 Dihedral : 6.287 58.940 1522 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.25 % Favored : 91.51 % Rotamer: Outliers : 3.57 % Allowed : 23.06 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.24), residues: 1242 helix: 0.49 (0.19), residues: 763 sheet: -0.14 (0.57), residues: 91 loop : -2.36 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 754 HIS 0.008 0.001 HIS A 759 PHE 0.022 0.001 PHE A 256 TYR 0.021 0.001 TYR A 388 ARG 0.002 0.000 ARG A1639 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.09 seconds wall clock time: 40 minutes 44.83 seconds (2444.83 seconds total)