Starting phenix.real_space_refine on Wed Feb 14 17:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/02_2024/8fth_29426_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 6200 2.51 5 N 1697 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 334": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A ASP 877": "OD1" <-> "OD2" Residue "A PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1200": "OD1" <-> "OD2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1292": "OE1" <-> "OE2" Residue "A TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1631": "OD1" <-> "OD2" Residue "A GLU 1655": "OE1" <-> "OE2" Residue "A PHE 1715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1832": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9780 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9753 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 51, 'TRANS': 1211} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.56 Number of scatterers: 9780 At special positions: 0 Unit cell: (71.1808, 89.1904, 180.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 1819 8.00 N 1697 7.00 C 6200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 3 sheets defined 55.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 274 through 290 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 309 through 318 removed outlier: 4.128A pdb=" N GLY A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 338 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 352 through 360 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 402 through 416 removed outlier: 4.565A pdb=" N SER A 406 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 408 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 522 removed outlier: 3.851A pdb=" N ALA A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 removed outlier: 3.740A pdb=" N PHE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.499A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 604 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 625 through 633 removed outlier: 3.609A pdb=" N ILE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.693A pdb=" N THR A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.781A pdb=" N SER A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 709 Proline residue: A 697 - end of helix removed outlier: 3.995A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 701 " --> pdb=" O PRO A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 724 through 751 removed outlier: 3.548A pdb=" N ALA A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N MET A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 784 removed outlier: 4.354A pdb=" N GLN A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASP A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 800 removed outlier: 3.712A pdb=" N LYS A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.588A pdb=" N ARG A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 807' Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 823 through 840 Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 879 through 886 Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1142 through 1166 Proline residue: A1151 - end of helix removed outlier: 3.630A pdb=" N GLU A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1201 Processing helix chain 'A' and resid 1272 through 1286 removed outlier: 5.256A pdb=" N GLN A1285 " --> pdb=" O LEU A1281 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1286 " --> pdb=" O GLU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1294 Processing helix chain 'A' and resid 1308 through 1316 removed outlier: 3.591A pdb=" N ASN A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 removed outlier: 3.895A pdb=" N ARG A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1326 " --> pdb=" O GLN A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1357 Processing helix chain 'A' and resid 1396 through 1408 Processing helix chain 'A' and resid 1435 through 1437 No H-bonds generated for 'chain 'A' and resid 1435 through 1437' Processing helix chain 'A' and resid 1440 through 1448 removed outlier: 3.723A pdb=" N ARG A1447 " --> pdb=" O LEU A1443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1448 " --> pdb=" O VAL A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1482 removed outlier: 3.628A pdb=" N ALA A1473 " --> pdb=" O GLY A1469 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A1475 " --> pdb=" O ILE A1471 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A1476 " --> pdb=" O LYS A1472 " (cutoff:3.500A) Proline residue: A1480 - end of helix Processing helix chain 'A' and resid 1495 through 1543 removed outlier: 3.987A pdb=" N LYS A1505 " --> pdb=" O PHE A1501 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A1506 " --> pdb=" O ASP A1502 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1507 " --> pdb=" O GLU A1503 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A1508 " --> pdb=" O LEU A1504 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1519 " --> pdb=" O ILE A1515 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A1522 " --> pdb=" O ASP A1518 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A1524 " --> pdb=" O ALA A1520 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A1530 " --> pdb=" O ALA A1526 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A1532 " --> pdb=" O GLU A1528 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A1538 " --> pdb=" O ARG A1534 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A1542 " --> pdb=" O GLN A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1555 No H-bonds generated for 'chain 'A' and resid 1553 through 1555' Processing helix chain 'A' and resid 1557 through 1559 No H-bonds generated for 'chain 'A' and resid 1557 through 1559' Processing helix chain 'A' and resid 1604 through 1607 No H-bonds generated for 'chain 'A' and resid 1604 through 1607' Processing helix chain 'A' and resid 1621 through 1627 Processing helix chain 'A' and resid 1648 through 1653 Processing helix chain 'A' and resid 1664 through 1667 No H-bonds generated for 'chain 'A' and resid 1664 through 1667' Processing helix chain 'A' and resid 1671 through 1674 Processing helix chain 'A' and resid 1702 through 1717 Processing helix chain 'A' and resid 1735 through 1749 Processing helix chain 'A' and resid 1752 through 1756 removed outlier: 3.568A pdb=" N GLU A1755 " --> pdb=" O SER A1752 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A1756 " --> pdb=" O ILE A1753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1752 through 1756' Processing helix chain 'A' and resid 1789 through 1801 removed outlier: 3.796A pdb=" N THR A1800 " --> pdb=" O ASN A1796 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A1801 " --> pdb=" O VAL A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1831 removed outlier: 3.809A pdb=" N ARG A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1839 through 1843 Processing sheet with id= A, first strand: chain 'A' and resid 1189 through 1193 removed outlier: 3.617A pdb=" N LYS A1232 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A1245 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A1230 " --> pdb=" O ARG A1245 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP A1207 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A1269 " --> pdb=" O ILE A1208 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A1210 " --> pdb=" O LYS A1267 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS A1267 " --> pdb=" O ILE A1210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1632 through 1635 removed outlier: 7.238A pdb=" N LEU A1337 " --> pdb=" O HIS A1633 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A1635 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN A1339 " --> pdb=" O LEU A1635 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A1340 " --> pdb=" O GLY A1597 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A1390 " --> pdb=" O ILE A1570 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP A1572 " --> pdb=" O LEU A1390 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS A1392 " --> pdb=" O ASP A1572 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1681 through 1683 removed outlier: 6.897A pdb=" N LEU A1806 " --> pdb=" O ARG A1682 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU A1758 " --> pdb=" O ILE A1730 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR A1732 " --> pdb=" O GLU A1758 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A1760 " --> pdb=" O THR A1732 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1290 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: 3.58 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1650 1.32 - 1.44: 2468 1.44 - 1.57: 5721 1.57 - 1.69: 3 1.69 - 1.82: 105 Bond restraints: 9947 Sorted by residual: bond pdb=" CA SER A 713 " pdb=" CB SER A 713 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.69e-02 3.50e+03 1.76e+01 bond pdb=" C ILE A1584 " pdb=" N PRO A1585 " ideal model delta sigma weight residual 1.334 1.412 -0.078 2.34e-02 1.83e+03 1.11e+01 bond pdb=" C PRO A 712 " pdb=" O PRO A 712 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" N LYS A1829 " pdb=" CA LYS A1829 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.52e+00 bond pdb=" N ARG A1831 " pdb=" CA ARG A1831 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.38e+00 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 94.18 - 102.60: 57 102.60 - 111.01: 3519 111.01 - 119.43: 5048 119.43 - 127.85: 4742 127.85 - 136.26: 88 Bond angle restraints: 13454 Sorted by residual: angle pdb=" N PRO A 712 " pdb=" CA PRO A 712 " pdb=" CB PRO A 712 " ideal model delta sigma weight residual 103.25 94.80 8.45 1.05e+00 9.07e-01 6.48e+01 angle pdb=" N VAL A1746 " pdb=" CA VAL A1746 " pdb=" C VAL A1746 " ideal model delta sigma weight residual 111.05 105.17 5.88 1.25e+00 6.40e-01 2.22e+01 angle pdb=" CA LEU A 566 " pdb=" CB LEU A 566 " pdb=" CG LEU A 566 " ideal model delta sigma weight residual 116.30 132.75 -16.45 3.50e+00 8.16e-02 2.21e+01 angle pdb=" C PRO A1671 " pdb=" CA PRO A1671 " pdb=" CB PRO A1671 " ideal model delta sigma weight residual 111.56 104.46 7.10 1.65e+00 3.67e-01 1.85e+01 angle pdb=" C ALA A 886 " pdb=" N LEU A 887 " pdb=" CA LEU A 887 " ideal model delta sigma weight residual 120.58 113.82 6.76 1.71e+00 3.42e-01 1.56e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 5477 24.77 - 49.54: 505 49.54 - 74.31: 70 74.31 - 99.08: 6 99.08 - 123.85: 1 Dihedral angle restraints: 6059 sinusoidal: 2388 harmonic: 3671 Sorted by residual: dihedral pdb=" O1B ADP A2101 " pdb=" O3A ADP A2101 " pdb=" PB ADP A2101 " pdb=" PA ADP A2101 " ideal model delta sinusoidal sigma weight residual -60.00 63.85 -123.85 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA THR A 411 " pdb=" C THR A 411 " pdb=" N SER A 412 " pdb=" CA SER A 412 " ideal model delta harmonic sigma weight residual -180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TYR A1654 " pdb=" C TYR A1654 " pdb=" N GLU A1655 " pdb=" CA GLU A1655 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 6056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1187 0.054 - 0.108: 275 0.108 - 0.161: 74 0.161 - 0.215: 10 0.215 - 0.269: 4 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA PHE A1648 " pdb=" N PHE A1648 " pdb=" C PHE A1648 " pdb=" CB PHE A1648 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB THR A1269 " pdb=" CA THR A1269 " pdb=" OG1 THR A1269 " pdb=" CG2 THR A1269 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLN A1670 " pdb=" N GLN A1670 " pdb=" C GLN A1670 " pdb=" CB GLN A1670 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1547 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 524 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C LYS A 524 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS A 524 " 0.035 2.00e-02 2.50e+03 pdb=" N PRO A 525 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 609 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 610 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 840 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLU A 840 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU A 840 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 841 " -0.024 2.00e-02 2.50e+03 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2810 2.82 - 3.34: 8594 3.34 - 3.86: 15528 3.86 - 4.38: 17612 4.38 - 4.90: 30767 Nonbonded interactions: 75311 Sorted by model distance: nonbonded pdb=" OD1 ASN A 772 " pdb=" OG1 THR A 830 " model vdw 2.298 2.440 nonbonded pdb=" O ALA A1279 " pdb=" OG SER A1283 " model vdw 2.305 2.440 nonbonded pdb=" O GLU A1156 " pdb=" OG SER A1160 " model vdw 2.310 2.440 nonbonded pdb=" O SER A1554 " pdb=" OH TYR A1588 " model vdw 2.315 2.440 nonbonded pdb=" O ALA A1164 " pdb=" OG1 THR A1168 " model vdw 2.320 2.440 ... (remaining 75306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 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: 13.850 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.006 0.078 9947 Z= 0.366 Angle : 1.008 16.453 13454 Z= 0.534 Chirality : 0.052 0.269 1550 Planarity : 0.008 0.114 1717 Dihedral : 18.199 123.854 3663 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.28 % Favored : 94.23 % Rotamer: Outliers : 1.28 % Allowed : 26.59 % Favored : 72.13 % 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: -2.58 (0.21), residues: 1231 helix: -1.39 (0.16), residues: 733 sheet: -0.91 (0.55), residues: 106 loop : -2.28 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1672 HIS 0.009 0.002 HIS A 415 PHE 0.026 0.003 PHE A1304 TYR 0.016 0.002 TYR A1681 ARG 0.006 0.001 ARG A1640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.7741 (mmm) cc_final: 0.7046 (mtp) REVERT: A 843 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6985 (mtp) REVERT: A 1290 MET cc_start: 0.6608 (tpp) cc_final: 0.6363 (mmt) REVERT: A 1317 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6683 (pt0) REVERT: A 1714 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6481 (ttt180) REVERT: A 1830 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7333 (tp-100) outliers start: 13 outliers final: 5 residues processed: 146 average time/residue: 0.2558 time to fit residues: 51.3061 Evaluate side-chains 147 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 712 PRO Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 60 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9947 Z= 0.182 Angle : 0.566 10.001 13454 Z= 0.281 Chirality : 0.039 0.189 1550 Planarity : 0.005 0.075 1717 Dihedral : 6.716 112.029 1375 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.55 % Allowed : 26.40 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1231 helix: 0.11 (0.19), residues: 741 sheet: -0.52 (0.57), residues: 103 loop : -2.07 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.006 0.001 HIS A1673 PHE 0.019 0.001 PHE A1648 TYR 0.011 0.001 TYR A1145 ARG 0.003 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.240 Fit side-chains REVERT: A 366 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.6880 (ttt-90) REVERT: A 663 MET cc_start: 0.8278 (mmm) cc_final: 0.8074 (mmt) REVERT: A 1714 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6541 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7358 (tm-30) outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 0.2510 time to fit residues: 56.8216 Evaluate side-chains 155 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9947 Z= 0.224 Angle : 0.592 10.178 13454 Z= 0.292 Chirality : 0.040 0.150 1550 Planarity : 0.005 0.062 1717 Dihedral : 6.297 114.305 1361 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.93 % Allowed : 25.91 % Favored : 70.17 % 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: -0.30 (0.25), residues: 1231 helix: 0.74 (0.20), residues: 746 sheet: -0.56 (0.57), residues: 104 loop : -1.94 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.005 0.001 HIS A 727 PHE 0.023 0.001 PHE A1648 TYR 0.015 0.001 TYR A1145 ARG 0.003 0.000 ARG A1833 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.200 Fit side-chains REVERT: A 366 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.6859 (ttt-90) REVERT: A 1714 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6592 (ttt180) REVERT: A 1830 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7324 (tm-30) outliers start: 40 outliers final: 24 residues processed: 173 average time/residue: 0.2541 time to fit residues: 60.3386 Evaluate side-chains 164 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.4980 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9947 Z= 0.197 Angle : 0.557 9.237 13454 Z= 0.275 Chirality : 0.039 0.165 1550 Planarity : 0.004 0.057 1717 Dihedral : 6.111 110.370 1361 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.02 % Allowed : 25.71 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1231 helix: 1.02 (0.20), residues: 744 sheet: -0.56 (0.57), residues: 104 loop : -1.87 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.009 0.001 HIS A 415 PHE 0.019 0.001 PHE A1648 TYR 0.014 0.001 TYR A1145 ARG 0.003 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.261 Fit side-chains REVERT: A 532 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6729 (ttm170) REVERT: A 1560 LYS cc_start: 0.6390 (tppt) cc_final: 0.6077 (tppt) REVERT: A 1714 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6561 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7330 (tm-30) outliers start: 41 outliers final: 26 residues processed: 175 average time/residue: 0.2555 time to fit residues: 62.0755 Evaluate side-chains 165 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9947 Z= 0.178 Angle : 0.546 8.421 13454 Z= 0.267 Chirality : 0.038 0.155 1550 Planarity : 0.004 0.054 1717 Dihedral : 5.940 107.108 1361 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.02 % Allowed : 25.52 % Favored : 70.46 % 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: 0.18 (0.25), residues: 1231 helix: 1.22 (0.20), residues: 742 sheet: -0.58 (0.57), residues: 104 loop : -1.86 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.004 0.001 HIS A 727 PHE 0.019 0.001 PHE A1648 TYR 0.012 0.001 TYR A1145 ARG 0.004 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 532 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6767 (ttm170) REVERT: A 682 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7749 (tt) REVERT: A 1330 LYS cc_start: 0.6842 (tttt) cc_final: 0.6448 (ttmt) REVERT: A 1560 LYS cc_start: 0.6390 (tppt) cc_final: 0.6085 (tppt) REVERT: A 1714 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6601 (ttt180) REVERT: A 1830 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7316 (tm-30) outliers start: 41 outliers final: 32 residues processed: 174 average time/residue: 0.2345 time to fit residues: 57.0865 Evaluate side-chains 173 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 chunk 24 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9947 Z= 0.163 Angle : 0.530 7.816 13454 Z= 0.259 Chirality : 0.038 0.150 1550 Planarity : 0.004 0.052 1717 Dihedral : 5.778 104.545 1361 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.22 % Allowed : 25.52 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1231 helix: 1.36 (0.20), residues: 741 sheet: -0.57 (0.57), residues: 104 loop : -1.77 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.005 0.001 HIS A 415 PHE 0.019 0.001 PHE A1648 TYR 0.011 0.001 TYR A1145 ARG 0.003 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 1.000 Fit side-chains REVERT: A 682 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 796 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6629 (mptt) REVERT: A 1330 LYS cc_start: 0.6853 (tttt) cc_final: 0.6419 (ttmt) REVERT: A 1543 LYS cc_start: 0.6684 (mttp) cc_final: 0.6444 (mttm) REVERT: A 1560 LYS cc_start: 0.6386 (tppt) cc_final: 0.6092 (tppt) REVERT: A 1714 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6596 (ttt180) REVERT: A 1830 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7359 (tm-30) outliers start: 43 outliers final: 32 residues processed: 178 average time/residue: 0.2270 time to fit residues: 56.0961 Evaluate side-chains 174 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.0050 chunk 89 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 0.0870 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9947 Z= 0.148 Angle : 0.521 7.753 13454 Z= 0.253 Chirality : 0.037 0.137 1550 Planarity : 0.004 0.051 1717 Dihedral : 5.601 101.457 1361 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.43 % Allowed : 26.40 % Favored : 70.17 % 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: 0.51 (0.25), residues: 1231 helix: 1.49 (0.20), residues: 741 sheet: -0.56 (0.57), residues: 104 loop : -1.71 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.012 0.001 HIS A 415 PHE 0.018 0.001 PHE A1648 TYR 0.009 0.001 TYR A1145 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 0.985 Fit side-chains REVERT: A 682 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 796 LYS cc_start: 0.7412 (mmmt) cc_final: 0.6592 (mptt) REVERT: A 1330 LYS cc_start: 0.6837 (tttt) cc_final: 0.6413 (ttmt) REVERT: A 1448 MET cc_start: 0.8378 (mmt) cc_final: 0.7873 (mmt) REVERT: A 1543 LYS cc_start: 0.6612 (mttp) cc_final: 0.6407 (mttm) REVERT: A 1560 LYS cc_start: 0.6391 (tppt) cc_final: 0.6105 (tppt) REVERT: A 1647 ARG cc_start: 0.5915 (ptt180) cc_final: 0.5708 (ptt180) REVERT: A 1649 PRO cc_start: 0.7673 (Cg_endo) cc_final: 0.7424 (Cg_exo) REVERT: A 1714 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6603 (ttt180) REVERT: A 1826 GLU cc_start: 0.6151 (pp20) cc_final: 0.5779 (pp20) REVERT: A 1830 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7409 (tm-30) outliers start: 35 outliers final: 31 residues processed: 171 average time/residue: 0.2433 time to fit residues: 57.0691 Evaluate side-chains 178 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9947 Z= 0.224 Angle : 0.578 8.080 13454 Z= 0.283 Chirality : 0.039 0.147 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.865 110.323 1361 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.93 % Allowed : 25.52 % Favored : 70.56 % 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: 0.36 (0.25), residues: 1231 helix: 1.31 (0.20), residues: 756 sheet: -0.63 (0.56), residues: 104 loop : -1.74 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 734 HIS 0.016 0.001 HIS A 415 PHE 0.026 0.001 PHE A1648 TYR 0.015 0.001 TYR A1145 ARG 0.006 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 1.136 Fit side-chains REVERT: A 682 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 796 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6636 (mptt) REVERT: A 1543 LYS cc_start: 0.6714 (mttp) cc_final: 0.6491 (mttm) REVERT: A 1560 LYS cc_start: 0.6433 (tppt) cc_final: 0.6160 (tppt) REVERT: A 1714 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6550 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6191 (pp20) cc_final: 0.5865 (pp20) REVERT: A 1830 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7344 (tm-30) outliers start: 40 outliers final: 35 residues processed: 176 average time/residue: 0.2428 time to fit residues: 59.4650 Evaluate side-chains 180 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9947 Z= 0.193 Angle : 0.554 7.723 13454 Z= 0.271 Chirality : 0.039 0.141 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.765 107.465 1361 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.83 % Allowed : 26.01 % Favored : 70.17 % 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: 0.45 (0.25), residues: 1231 helix: 1.42 (0.20), residues: 748 sheet: -0.62 (0.56), residues: 105 loop : -1.71 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 734 HIS 0.007 0.001 HIS A 415 PHE 0.018 0.001 PHE A1648 TYR 0.013 0.001 TYR A1145 ARG 0.002 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5996 (mm-30) REVERT: A 682 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 1543 LYS cc_start: 0.6709 (mttp) cc_final: 0.6485 (mttm) REVERT: A 1560 LYS cc_start: 0.6448 (tppt) cc_final: 0.6162 (tppt) REVERT: A 1714 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6585 (ttt180) REVERT: A 1826 GLU cc_start: 0.6197 (pp20) cc_final: 0.5875 (pp20) REVERT: A 1830 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7467 (tm-30) outliers start: 39 outliers final: 34 residues processed: 174 average time/residue: 0.2459 time to fit residues: 58.9379 Evaluate side-chains 180 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.0770 chunk 115 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.0020 chunk 106 optimal weight: 1.9990 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9947 Z= 0.154 Angle : 0.530 7.612 13454 Z= 0.259 Chirality : 0.038 0.137 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.532 101.655 1361 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.14 % Allowed : 26.79 % Favored : 70.07 % 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: 0.65 (0.25), residues: 1231 helix: 1.59 (0.20), residues: 741 sheet: -0.61 (0.56), residues: 106 loop : -1.57 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 734 HIS 0.011 0.001 HIS A 415 PHE 0.018 0.001 PHE A1648 TYR 0.010 0.001 TYR A1145 ARG 0.003 0.000 ARG A1831 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.008 Fit side-chains REVERT: A 418 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5954 (mm-30) REVERT: A 682 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 796 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6564 (mptt) REVERT: A 1543 LYS cc_start: 0.6627 (mttp) cc_final: 0.6424 (mttm) REVERT: A 1560 LYS cc_start: 0.6429 (tppt) cc_final: 0.6153 (tppt) REVERT: A 1649 PRO cc_start: 0.7696 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: A 1714 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6607 (ttt180) REVERT: A 1826 GLU cc_start: 0.6142 (pp20) cc_final: 0.5824 (pp20) REVERT: A 1830 GLN cc_start: 0.7760 (tm130) cc_final: 0.7538 (tm-30) outliers start: 32 outliers final: 30 residues processed: 169 average time/residue: 0.2448 time to fit residues: 56.7913 Evaluate side-chains 174 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.3980 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.199453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.170201 restraints weight = 12105.668| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.89 r_work: 0.3914 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9947 Z= 0.214 Angle : 0.569 7.760 13454 Z= 0.278 Chirality : 0.039 0.146 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.377 107.564 1358 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.83 % Allowed : 26.20 % Favored : 69.97 % 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: 0.48 (0.25), residues: 1231 helix: 1.44 (0.20), residues: 750 sheet: -0.71 (0.55), residues: 106 loop : -1.68 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1672 HIS 0.013 0.001 HIS A 415 PHE 0.017 0.001 PHE A1648 TYR 0.014 0.001 TYR A1145 ARG 0.006 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.17 seconds wall clock time: 48 minutes 36.47 seconds (2916.47 seconds total)