Starting phenix.real_space_refine on Sat Mar 16 07:29:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/03_2024/7yxy_14369.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.045 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 96 5.16 5 C 8988 2.51 5 N 2403 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 470": "OD1" <-> "OD2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 784": "OD1" <-> "OD2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1818": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14031 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14031 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1739, 14020 Classifications: {'peptide': 1739} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1670} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1739, 14020 Classifications: {'peptide': 1739} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1670} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14311 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A1745 " occ=0.40 Time building chain proxies: 13.72, per 1000 atoms: 0.98 Number of scatterers: 14031 At special positions: 0 Unit cell: (133.952, 141.44, 158.08, 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 96 16.00 O 2544 8.00 N 2403 7.00 C 8988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2471 " - pdb=" SG CYS A2474 " distance=2.04 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: 5.15 Conformation dependent library (CDL) restraints added in 4.7 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3314 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 9 sheets defined 67.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 382 through 394 removed outlier: 4.019A pdb=" N MET A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.511A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 4.092A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 461 through 479 removed outlier: 3.610A pdb=" N ASN A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.221A pdb=" N LYS A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 539 removed outlier: 3.590A pdb=" N TYR A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.831A pdb=" N LEU A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 4.417A pdb=" N ASN A 604 " --> pdb=" O HIS A 600 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 632 removed outlier: 3.653A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 3.608A pdb=" N GLU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 682 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.811A pdb=" N ARG A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 4.010A pdb=" N GLU A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 751 removed outlier: 3.519A pdb=" N ARG A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.617A pdb=" N TRP A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 807 through 831 removed outlier: 3.662A pdb=" N ILE A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.519A pdb=" N ALA A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 4.276A pdb=" N ILE A1018 " --> pdb=" O HIS A1014 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.906A pdb=" N ARG A1037 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1066 Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1084 through 1100 removed outlier: 3.889A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1121 removed outlier: 3.582A pdb=" N HIS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1121 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.775A pdb=" N LEU A1130 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1164 removed outlier: 3.656A pdb=" N LEU A1157 " --> pdb=" O LYS A1153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1251 removed outlier: 3.632A pdb=" N CYS A1251 " --> pdb=" O TRP A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1257 removed outlier: 5.992A pdb=" N GLN A1255 " --> pdb=" O GLY A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1269 removed outlier: 3.928A pdb=" N THR A1265 " --> pdb=" O ASN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1299 removed outlier: 3.665A pdb=" N VAL A1284 " --> pdb=" O GLU A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1307 removed outlier: 4.027A pdb=" N ASP A1304 " --> pdb=" O PRO A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1321 Processing helix chain 'A' and resid 1325 through 1342 removed outlier: 3.610A pdb=" N ARG A1329 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1359 Processing helix chain 'A' and resid 1364 through 1369 Processing helix chain 'A' and resid 1374 through 1389 Processing helix chain 'A' and resid 1396 through 1417 Processing helix chain 'A' and resid 1423 through 1438 Processing helix chain 'A' and resid 1457 through 1466 Processing helix chain 'A' and resid 1468 through 1479 removed outlier: 3.698A pdb=" N ASN A1472 " --> pdb=" O PHE A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1512 through 1528 removed outlier: 3.929A pdb=" N GLN A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1577 removed outlier: 4.398A pdb=" N VAL A1571 " --> pdb=" O TYR A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1587 removed outlier: 3.675A pdb=" N LEU A1586 " --> pdb=" O ARG A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1657 Processing helix chain 'A' and resid 1664 through 1671 removed outlier: 3.511A pdb=" N PHE A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1704 removed outlier: 3.622A pdb=" N PHE A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1714 Processing helix chain 'A' and resid 1749 through 1760 removed outlier: 3.536A pdb=" N TYR A1757 " --> pdb=" O SER A1753 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1768 Processing helix chain 'A' and resid 1825 through 1827 No H-bonds generated for 'chain 'A' and resid 1825 through 1827' Processing helix chain 'A' and resid 1828 through 1837 Processing helix chain 'A' and resid 1912 through 1920 Processing helix chain 'A' and resid 1988 through 2005 removed outlier: 3.720A pdb=" N ARG A1992 " --> pdb=" O GLU A1988 " (cutoff:3.500A) Processing helix chain 'A' and resid 2006 through 2019 Processing helix chain 'A' and resid 2020 through 2024 Processing helix chain 'A' and resid 2034 through 2056 Processing helix chain 'A' and resid 2060 through 2065 Processing helix chain 'A' and resid 2067 through 2079 Processing helix chain 'A' and resid 2081 through 2093 removed outlier: 3.610A pdb=" N ARG A2085 " --> pdb=" O SER A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2105 Processing helix chain 'A' and resid 2109 through 2127 Processing helix chain 'A' and resid 2151 through 2163 removed outlier: 3.634A pdb=" N LEU A2163 " --> pdb=" O ALA A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2171 Processing helix chain 'A' and resid 2175 through 2188 removed outlier: 3.593A pdb=" N PHE A2179 " --> pdb=" O LEU A2175 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2199 Processing helix chain 'A' and resid 2200 through 2208 Processing helix chain 'A' and resid 2225 through 2238 removed outlier: 3.548A pdb=" N CYS A2238 " --> pdb=" O GLN A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2280 removed outlier: 3.866A pdb=" N ILE A2278 " --> pdb=" O ASN A2274 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2292 Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 4.016A pdb=" N VAL A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A2301 " --> pdb=" O GLU A2297 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2327 Processing helix chain 'A' and resid 2329 through 2332 Processing helix chain 'A' and resid 2333 through 2345 Processing helix chain 'A' and resid 2350 through 2360 Processing helix chain 'A' and resid 2368 through 2377 Processing helix chain 'A' and resid 2380 through 2398 removed outlier: 3.811A pdb=" N ALA A2384 " --> pdb=" O TYR A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2399 through 2404 removed outlier: 3.582A pdb=" N GLN A2403 " --> pdb=" O PRO A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2428 Processing helix chain 'A' and resid 2463 through 2471 removed outlier: 3.688A pdb=" N CYS A2471 " --> pdb=" O LEU A2467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA2, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.706A pdb=" N GLY A1558 " --> pdb=" O TYR A1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1672 through 1673 Processing sheet with id=AA4, first strand: chain 'A' and resid 1730 through 1737 removed outlier: 6.842A pdb=" N SER A1717 " --> pdb=" O LYS A1787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1740 through 1743 removed outlier: 6.066A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A1798 " --> pdb=" O LEU A1740 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A1742 " --> pdb=" O LYS A1798 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1740 through 1743 removed outlier: 6.066A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A1798 " --> pdb=" O LEU A1740 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A1742 " --> pdb=" O LYS A1798 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A1866 " --> pdb=" O ILE A1885 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1769 through 1771 removed outlier: 3.718A pdb=" N LYS A1776 " --> pdb=" O CYS A1771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1800 through 1803 Processing sheet with id=AA9, first strand: chain 'A' and resid 1924 through 1931 removed outlier: 3.526A pdb=" N SER A1938 " --> pdb=" O VAL A1929 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A1931 " --> pdb=" O ARG A1936 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2448 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: 5.79 Time building geometry restraints manager: 5.61 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: 4575 1.35 - 1.47: 3329 1.47 - 1.59: 6288 1.59 - 1.71: 1 1.71 - 1.83: 142 Bond restraints: 14335 Sorted by residual: bond pdb=" CB PRO A1083 " pdb=" CG PRO A1083 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 7.01e+00 bond pdb=" C MET A1233 " pdb=" N PRO A1234 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.27e-02 6.20e+03 5.55e+00 bond pdb=" C ALA A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.30e-02 5.92e+03 3.66e+00 bond pdb=" N PRO A1664 " pdb=" CA PRO A1664 " ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 2.03e+00 bond pdb=" N GLU A1290 " pdb=" CA GLU A1290 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.21e-02 6.83e+03 1.02e+00 ... (remaining 14330 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.49: 265 105.49 - 112.66: 7449 112.66 - 119.83: 4905 119.83 - 127.00: 6604 127.00 - 134.17: 168 Bond angle restraints: 19391 Sorted by residual: angle pdb=" N TYR A2402 " pdb=" CA TYR A2402 " pdb=" C TYR A2402 " ideal model delta sigma weight residual 114.62 107.20 7.42 1.14e+00 7.69e-01 4.23e+01 angle pdb=" CA PRO A1083 " pdb=" N PRO A1083 " pdb=" CD PRO A1083 " ideal model delta sigma weight residual 112.00 103.68 8.32 1.40e+00 5.10e-01 3.53e+01 angle pdb=" N ILE A1529 " pdb=" CA ILE A1529 " pdb=" C ILE A1529 " ideal model delta sigma weight residual 113.42 109.03 4.39 1.17e+00 7.31e-01 1.41e+01 angle pdb=" N GLU A1290 " pdb=" CA GLU A1290 " pdb=" CB GLU A1290 " ideal model delta sigma weight residual 110.12 115.34 -5.22 1.47e+00 4.63e-01 1.26e+01 angle pdb=" N VAL A2096 " pdb=" CA VAL A2096 " pdb=" C VAL A2096 " ideal model delta sigma weight residual 113.42 109.37 4.05 1.17e+00 7.31e-01 1.20e+01 ... (remaining 19386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7820 17.68 - 35.36: 668 35.36 - 53.04: 103 53.04 - 70.72: 34 70.72 - 88.41: 13 Dihedral angle restraints: 8638 sinusoidal: 3533 harmonic: 5105 Sorted by residual: dihedral pdb=" CA CYS A2471 " pdb=" C CYS A2471 " pdb=" N GLU A2472 " pdb=" CA GLU A2472 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ALA A1456 " pdb=" C ALA A1456 " pdb=" N ASN A1457 " pdb=" CA ASN A1457 " ideal model delta harmonic sigma weight residual 180.00 -159.51 -20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TRP A 565 " pdb=" C TRP A 565 " pdb=" N VAL A 566 " pdb=" CA VAL A 566 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 8635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1481 0.036 - 0.072: 498 0.072 - 0.108: 144 0.108 - 0.144: 20 0.144 - 0.181: 2 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CA PRO A1083 " pdb=" N PRO A1083 " pdb=" C PRO A1083 " pdb=" CB PRO A1083 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE A1299 " pdb=" CA ILE A1299 " pdb=" CG1 ILE A1299 " pdb=" CG2 ILE A1299 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB VAL A 853 " pdb=" CA VAL A 853 " pdb=" CG1 VAL A 853 " pdb=" CG2 VAL A 853 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2142 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1082 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A1083 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1047 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1048 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1048 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1048 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A2257 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A2258 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A2258 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2258 " -0.029 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1971 2.76 - 3.29: 14111 3.29 - 3.83: 23847 3.83 - 4.36: 27466 4.36 - 4.90: 46972 Nonbonded interactions: 114367 Sorted by model distance: nonbonded pdb=" O ASP A 543 " pdb=" NE2 GLN A 547 " model vdw 2.219 2.520 nonbonded pdb=" O GLU A1452 " pdb=" ND2 ASN A1457 " model vdw 2.231 2.520 nonbonded pdb=" O VAL A2160 " pdb=" OH TYR A2178 " model vdw 2.233 2.440 nonbonded pdb=" O PRO A1790 " pdb=" OH TYR A1863 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A2185 " pdb=" OE1 GLN A2195 " model vdw 2.243 2.440 ... (remaining 114362 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=0.40 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: 4.050 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: 18.690 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 49.430 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.003 0.132 14335 Z= 0.176 Angle : 0.593 10.400 19391 Z= 0.326 Chirality : 0.039 0.181 2145 Planarity : 0.005 0.103 2478 Dihedral : 13.929 88.405 5321 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.42 (0.21), residues: 1708 helix: 1.06 (0.16), residues: 1085 sheet: 0.49 (0.58), residues: 98 loop : -1.35 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 700 HIS 0.004 0.001 HIS A2032 PHE 0.030 0.002 PHE A 740 TYR 0.025 0.001 TYR A1567 ARG 0.016 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.676 Fit side-chains REVERT: A 720 PHE cc_start: 0.4904 (t80) cc_final: 0.4264 (t80) REVERT: A 763 MET cc_start: 0.3093 (ptt) cc_final: 0.2116 (tpt) REVERT: A 1233 MET cc_start: 0.5742 (mmm) cc_final: 0.5445 (mmm) REVERT: A 1567 TYR cc_start: 0.7877 (p90) cc_final: 0.7488 (p90) REVERT: A 1576 TYR cc_start: 0.6665 (t80) cc_final: 0.6456 (t80) REVERT: A 1933 MET cc_start: 0.2149 (pmm) cc_final: 0.0990 (mtm) REVERT: A 1956 MET cc_start: 0.6077 (mpp) cc_final: 0.5760 (mtp) REVERT: A 2364 ASP cc_start: 0.4779 (m-30) cc_final: 0.4279 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2651 time to fit residues: 61.1513 Evaluate side-chains 106 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1114 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS A2177 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14335 Z= 0.290 Angle : 0.646 10.910 19391 Z= 0.333 Chirality : 0.042 0.161 2145 Planarity : 0.005 0.066 2478 Dihedral : 4.574 28.961 1885 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 1.05 % Allowed : 5.10 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1708 helix: 0.95 (0.16), residues: 1093 sheet: 0.77 (0.56), residues: 96 loop : -1.25 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.026 0.002 PHE A 719 TYR 0.019 0.002 TYR A1662 ARG 0.015 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.722 Fit side-chains REVERT: A 720 PHE cc_start: 0.5403 (t80) cc_final: 0.4694 (t80) REVERT: A 763 MET cc_start: 0.2724 (ptt) cc_final: 0.1984 (tpt) REVERT: A 1461 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 1568 MET cc_start: 0.8212 (ptp) cc_final: 0.7996 (ptp) REVERT: A 1933 MET cc_start: 0.2074 (pmm) cc_final: 0.0928 (mtm) REVERT: A 1956 MET cc_start: 0.6099 (mpp) cc_final: 0.5889 (mtt) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.2390 time to fit residues: 47.6121 Evaluate side-chains 118 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1313 GLN A1574 GLN ** A2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14335 Z= 0.185 Angle : 0.570 8.924 19391 Z= 0.293 Chirality : 0.039 0.147 2145 Planarity : 0.004 0.060 2478 Dihedral : 4.421 27.858 1885 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 0.92 % Allowed : 7.52 % Favored : 91.57 % 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: 0.63 (0.21), residues: 1708 helix: 1.20 (0.16), residues: 1092 sheet: 0.73 (0.55), residues: 96 loop : -1.30 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1897 HIS 0.003 0.001 HIS A2032 PHE 0.019 0.002 PHE A 743 TYR 0.017 0.001 TYR A1662 ARG 0.005 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.579 Fit side-chains REVERT: A 720 PHE cc_start: 0.5403 (t80) cc_final: 0.4785 (t80) REVERT: A 737 MET cc_start: 0.6970 (tpp) cc_final: 0.6108 (tpt) REVERT: A 763 MET cc_start: 0.2700 (ptt) cc_final: 0.2016 (tpt) REVERT: A 773 TYR cc_start: 0.7205 (m-10) cc_final: 0.4969 (t80) REVERT: A 775 TRP cc_start: 0.5867 (m100) cc_final: 0.5156 (t-100) REVERT: A 860 TYR cc_start: 0.7179 (t80) cc_final: 0.6812 (t80) REVERT: A 1100 MET cc_start: 0.4725 (ttm) cc_final: 0.3588 (ppp) REVERT: A 1665 ARG cc_start: 0.7580 (mmm160) cc_final: 0.6862 (mtm110) REVERT: A 1824 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6219 (tpt) REVERT: A 1910 MET cc_start: 0.5055 (ppp) cc_final: 0.4714 (ppp) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 0.2403 time to fit residues: 48.0886 Evaluate side-chains 121 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.3980 chunk 118 optimal weight: 0.2980 chunk 81 optimal weight: 0.4980 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 HIS A1064 HIS A1371 HIS A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14335 Z= 0.173 Angle : 0.560 9.267 19391 Z= 0.285 Chirality : 0.039 0.139 2145 Planarity : 0.004 0.056 2478 Dihedral : 4.310 27.266 1885 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 0.92 % Allowed : 8.43 % Favored : 90.65 % 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: 0.71 (0.21), residues: 1708 helix: 1.28 (0.16), residues: 1088 sheet: 0.70 (0.55), residues: 96 loop : -1.28 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1247 HIS 0.004 0.001 HIS A2000 PHE 0.024 0.002 PHE A1690 TYR 0.013 0.001 TYR A2178 ARG 0.004 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.575 Fit side-chains REVERT: A 720 PHE cc_start: 0.5377 (t80) cc_final: 0.4653 (t80) REVERT: A 737 MET cc_start: 0.6884 (tpp) cc_final: 0.5989 (tpt) REVERT: A 763 MET cc_start: 0.2872 (ptt) cc_final: 0.2223 (tpt) REVERT: A 773 TYR cc_start: 0.7163 (m-10) cc_final: 0.4971 (t80) REVERT: A 775 TRP cc_start: 0.5851 (m100) cc_final: 0.5133 (t-100) REVERT: A 860 TYR cc_start: 0.7240 (t80) cc_final: 0.6917 (t80) REVERT: A 1100 MET cc_start: 0.4660 (ttm) cc_final: 0.3120 (ppp) REVERT: A 1461 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 1665 ARG cc_start: 0.7493 (mmm160) cc_final: 0.6876 (mtm110) REVERT: A 1824 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6257 (tpt) REVERT: A 1910 MET cc_start: 0.4909 (ppp) cc_final: 0.2252 (ttt) REVERT: A 1933 MET cc_start: 0.2357 (pmm) cc_final: 0.1037 (mtm) outliers start: 14 outliers final: 5 residues processed: 124 average time/residue: 0.2304 time to fit residues: 45.0371 Evaluate side-chains 119 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14335 Z= 0.228 Angle : 0.583 9.896 19391 Z= 0.298 Chirality : 0.040 0.151 2145 Planarity : 0.004 0.055 2478 Dihedral : 4.396 27.752 1885 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 1.18 % Allowed : 9.22 % Favored : 89.61 % 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: 0.64 (0.21), residues: 1708 helix: 1.22 (0.16), residues: 1089 sheet: 0.66 (0.54), residues: 96 loop : -1.28 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.020 0.002 PHE A 719 TYR 0.014 0.001 TYR A2178 ARG 0.004 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.595 Fit side-chains REVERT: A 700 TRP cc_start: 0.7310 (t60) cc_final: 0.6301 (t60) REVERT: A 720 PHE cc_start: 0.5471 (t80) cc_final: 0.5056 (t80) REVERT: A 725 LEU cc_start: 0.6148 (mt) cc_final: 0.5709 (pp) REVERT: A 737 MET cc_start: 0.7030 (tpp) cc_final: 0.6117 (tpt) REVERT: A 763 MET cc_start: 0.2984 (ptt) cc_final: 0.2216 (tpt) REVERT: A 773 TYR cc_start: 0.7250 (m-10) cc_final: 0.5099 (t80) REVERT: A 860 TYR cc_start: 0.7264 (t80) cc_final: 0.6959 (t80) REVERT: A 1100 MET cc_start: 0.4655 (ttm) cc_final: 0.3262 (ppp) REVERT: A 1461 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: A 1665 ARG cc_start: 0.7414 (mmm160) cc_final: 0.6922 (mtm110) REVERT: A 1824 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6212 (tpt) REVERT: A 1910 MET cc_start: 0.4697 (ppp) cc_final: 0.2346 (ttt) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.2246 time to fit residues: 45.8201 Evaluate side-chains 129 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2031 ASP Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14335 Z= 0.232 Angle : 0.593 11.495 19391 Z= 0.302 Chirality : 0.040 0.153 2145 Planarity : 0.004 0.055 2478 Dihedral : 4.446 28.111 1885 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 1.37 % Allowed : 9.74 % Favored : 88.89 % 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: 0.61 (0.21), residues: 1708 helix: 1.17 (0.16), residues: 1088 sheet: 0.67 (0.54), residues: 96 loop : -1.23 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.031 0.002 PHE A1690 TYR 0.025 0.001 TYR A1949 ARG 0.004 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.512 Fit side-chains REVERT: A 763 MET cc_start: 0.2917 (ptt) cc_final: 0.2249 (tpp) REVERT: A 773 TYR cc_start: 0.7334 (m-10) cc_final: 0.5067 (t80) REVERT: A 860 TYR cc_start: 0.7289 (t80) cc_final: 0.6980 (t80) REVERT: A 1100 MET cc_start: 0.4548 (ttm) cc_final: 0.3525 (ppp) REVERT: A 1457 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7413 (m110) REVERT: A 1461 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 1582 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.4584 (ptp-170) REVERT: A 1665 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7032 (mtm110) REVERT: A 1824 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.6154 (tpt) REVERT: A 1910 MET cc_start: 0.4566 (ppp) cc_final: 0.2426 (ttt) REVERT: A 1933 MET cc_start: 0.2668 (pmm) cc_final: 0.1236 (mtm) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.2333 time to fit residues: 50.8000 Evaluate side-chains 134 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2031 ASP Chi-restraints excluded: chain A residue 2188 LEU Chi-restraints excluded: chain A residue 2200 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 166 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14335 Z= 0.202 Angle : 0.583 14.569 19391 Z= 0.293 Chirality : 0.039 0.149 2145 Planarity : 0.004 0.054 2478 Dihedral : 4.387 27.672 1885 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 1.44 % Allowed : 10.13 % Favored : 88.43 % 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: 0.69 (0.21), residues: 1708 helix: 1.26 (0.16), residues: 1094 sheet: 0.68 (0.54), residues: 96 loop : -1.27 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.027 0.002 PHE A1690 TYR 0.019 0.001 TYR A1949 ARG 0.004 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.673 Fit side-chains REVERT: A 737 MET cc_start: 0.6993 (tpp) cc_final: 0.6118 (tpt) REVERT: A 763 MET cc_start: 0.2948 (ptt) cc_final: 0.2365 (tpt) REVERT: A 773 TYR cc_start: 0.7340 (m-10) cc_final: 0.5007 (t80) REVERT: A 814 ASP cc_start: 0.5435 (m-30) cc_final: 0.5099 (p0) REVERT: A 860 TYR cc_start: 0.7335 (t80) cc_final: 0.7110 (t80) REVERT: A 1100 MET cc_start: 0.4337 (ttm) cc_final: 0.3477 (ppp) REVERT: A 1457 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7347 (m110) REVERT: A 1461 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 1568 MET cc_start: 0.7812 (ptp) cc_final: 0.7176 (pmm) REVERT: A 1665 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6987 (mtm110) REVERT: A 1824 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6220 (tpt) REVERT: A 1910 MET cc_start: 0.4661 (ppp) cc_final: 0.2763 (ttt) REVERT: A 1933 MET cc_start: 0.2575 (pmm) cc_final: 0.1161 (mtm) outliers start: 22 outliers final: 13 residues processed: 140 average time/residue: 0.2330 time to fit residues: 51.6670 Evaluate side-chains 131 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2188 LEU Chi-restraints excluded: chain A residue 2200 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 GLN A1770 HIS ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 14335 Z= 0.559 Angle : 0.826 12.881 19391 Z= 0.423 Chirality : 0.051 0.280 2145 Planarity : 0.006 0.077 2478 Dihedral : 5.258 30.468 1885 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 1.50 % Allowed : 10.65 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.32 (0.20), residues: 1708 helix: 0.37 (0.15), residues: 1093 sheet: 0.34 (0.52), residues: 101 loop : -1.46 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1247 HIS 0.008 0.002 HIS A2000 PHE 0.028 0.003 PHE A 719 TYR 0.022 0.003 TYR A 623 ARG 0.007 0.001 ARG A2173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.736 Fit side-chains REVERT: A 451 ASP cc_start: 0.7008 (p0) cc_final: 0.6687 (p0) REVERT: A 744 PHE cc_start: 0.4441 (OUTLIER) cc_final: 0.3135 (t80) REVERT: A 763 MET cc_start: 0.2968 (ptt) cc_final: 0.2122 (ttm) REVERT: A 860 TYR cc_start: 0.7315 (t80) cc_final: 0.7052 (t80) REVERT: A 1100 MET cc_start: 0.4464 (ttm) cc_final: 0.3659 (ppp) REVERT: A 1457 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7579 (m110) REVERT: A 1461 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 1665 ARG cc_start: 0.7420 (mmm160) cc_final: 0.7143 (mtm110) REVERT: A 1824 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6109 (tpt) REVERT: A 1910 MET cc_start: 0.4711 (ppp) cc_final: 0.2698 (ttt) REVERT: A 1933 MET cc_start: 0.2565 (pmm) cc_final: 0.1059 (mtm) REVERT: A 2211 ASP cc_start: 0.7494 (m-30) cc_final: 0.7229 (m-30) REVERT: A 2339 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8898 (tp) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.2398 time to fit residues: 53.1424 Evaluate side-chains 135 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2031 ASP Chi-restraints excluded: chain A residue 2200 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2339 LEU Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14335 Z= 0.184 Angle : 0.607 12.192 19391 Z= 0.308 Chirality : 0.040 0.222 2145 Planarity : 0.004 0.061 2478 Dihedral : 4.714 29.324 1885 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 1.05 % Allowed : 11.76 % Favored : 87.19 % 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: 0.44 (0.21), residues: 1708 helix: 1.08 (0.16), residues: 1079 sheet: 0.43 (0.54), residues: 96 loop : -1.32 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 775 HIS 0.009 0.001 HIS A 650 PHE 0.029 0.002 PHE A1690 TYR 0.016 0.001 TYR A2178 ARG 0.004 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.421 Fit side-chains REVERT: A 451 ASP cc_start: 0.6968 (p0) cc_final: 0.6642 (p0) REVERT: A 737 MET cc_start: 0.7039 (tpp) cc_final: 0.6303 (tpt) REVERT: A 763 MET cc_start: 0.2922 (ptt) cc_final: 0.2404 (tpt) REVERT: A 773 TYR cc_start: 0.7273 (m-80) cc_final: 0.4931 (t80) REVERT: A 814 ASP cc_start: 0.5314 (m-30) cc_final: 0.5099 (p0) REVERT: A 860 TYR cc_start: 0.7280 (t80) cc_final: 0.7045 (t80) REVERT: A 1100 MET cc_start: 0.4191 (ttm) cc_final: 0.3696 (ppp) REVERT: A 1457 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7314 (m110) REVERT: A 1461 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 1568 MET cc_start: 0.7720 (ptp) cc_final: 0.7308 (pmm) REVERT: A 1665 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6959 (mtm110) REVERT: A 1824 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6349 (tpt) REVERT: A 1910 MET cc_start: 0.4841 (ppp) cc_final: 0.3078 (ttt) REVERT: A 1933 MET cc_start: 0.2765 (pmm) cc_final: 0.1306 (mtm) REVERT: A 2339 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8772 (tp) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2193 time to fit residues: 47.0947 Evaluate side-chains 131 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2200 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2339 LEU Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 GLN ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14335 Z= 0.282 Angle : 0.639 12.066 19391 Z= 0.326 Chirality : 0.042 0.199 2145 Planarity : 0.005 0.061 2478 Dihedral : 4.716 28.874 1885 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 1.24 % Allowed : 11.44 % Favored : 87.32 % 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 (0.20), residues: 1708 helix: 1.00 (0.16), residues: 1082 sheet: 0.33 (0.54), residues: 96 loop : -1.29 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 775 HIS 0.006 0.001 HIS A2000 PHE 0.026 0.002 PHE A1690 TYR 0.022 0.002 TYR A1949 ARG 0.005 0.001 ARG A 742 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.645 Fit side-chains REVERT: A 451 ASP cc_start: 0.6996 (p0) cc_final: 0.6652 (p0) REVERT: A 655 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6317 (mt0) REVERT: A 737 MET cc_start: 0.7009 (tpp) cc_final: 0.6264 (tpt) REVERT: A 763 MET cc_start: 0.3094 (ptt) cc_final: 0.2476 (tpt) REVERT: A 773 TYR cc_start: 0.7286 (m-80) cc_final: 0.5023 (t80) REVERT: A 1100 MET cc_start: 0.4211 (ttm) cc_final: 0.3691 (ppp) REVERT: A 1266 LYS cc_start: 0.8062 (mttp) cc_final: 0.7620 (mttp) REVERT: A 1457 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7393 (m110) REVERT: A 1461 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 1568 MET cc_start: 0.7777 (ptp) cc_final: 0.7299 (pmm) REVERT: A 1665 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6988 (mtm110) REVERT: A 1824 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6370 (tpt) REVERT: A 1910 MET cc_start: 0.4819 (ppp) cc_final: 0.3055 (ttt) REVERT: A 2339 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8803 (tp) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.2291 time to fit residues: 47.7140 Evaluate side-chains 134 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1824 MET Chi-restraints excluded: chain A residue 2200 SER Chi-restraints excluded: chain A residue 2222 TYR Chi-restraints excluded: chain A residue 2274 ASN Chi-restraints excluded: chain A residue 2339 LEU Chi-restraints excluded: chain A residue 2471 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.0370 chunk 20 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.0970 chunk 120 optimal weight: 10.0000 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 GLN ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 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 = 0.4524 r_free = 0.4524 target = 0.192696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135915 restraints weight = 35852.583| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.13 r_work: 0.3578 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.294 14335 Z= 0.309 Angle : 0.840 59.200 19391 Z= 0.463 Chirality : 0.041 0.384 2145 Planarity : 0.005 0.061 2478 Dihedral : 4.731 28.833 1885 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 1.18 % Allowed : 11.50 % Favored : 87.32 % Cbeta Deviations : 0.06 % 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: 0.37 (0.21), residues: 1708 helix: 1.01 (0.16), residues: 1081 sheet: 0.33 (0.54), residues: 96 loop : -1.30 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 775 HIS 0.006 0.001 HIS A2000 PHE 0.025 0.002 PHE A1690 TYR 0.014 0.001 TYR A2178 ARG 0.004 0.000 ARG A1582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.57 seconds wall clock time: 57 minutes 11.75 seconds (3431.75 seconds total)