Starting phenix.real_space_refine on Sun Dec 10 09:22:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/12_2023/7yxy_14369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/12_2023/7yxy_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_14369/12_2023/7yxy_14369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/12_2023/7yxy_14369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/12_2023/7yxy_14369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxy_14369/12_2023/7yxy_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-1.21rc1-5172/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: 13.66, per 1000 atoms: 0.97 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: 5.28 Conformation dependent library (CDL) restraints added in 5.2 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: 1.77 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: 5.61 Time building geometry restraints manager: 5.73 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: 8.180 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: 18.990 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 49.200 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.220 ------------------------------------------------------------------------------- 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 : 1.590 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2803 time to fit residues: 64.5753 Evaluate side-chains 106 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3784 ------------------------------------------------------------------------------- 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 ** A2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS A2177 GLN A2351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14335 Z= 0.288 Angle : 0.641 11.436 19391 Z= 0.330 Chirality : 0.042 0.158 2145 Planarity : 0.005 0.063 2478 Dihedral : 4.532 28.437 1885 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.98 % Allowed : 5.29 % Favored : 93.73 % 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: 0.99 (0.16), residues: 1092 sheet: 0.79 (0.56), residues: 96 loop : -1.24 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.024 0.002 PHE A 720 TYR 0.029 0.002 TYR A1567 ARG 0.009 0.001 ARG A1665 *********************** 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 138 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.537 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.2358 time to fit residues: 47.9839 Evaluate side-chains 120 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2244 time to fit residues: 5.3081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 170 optimal weight: 0.0370 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1313 GLN A1574 GLN A2011 GLN A2351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14335 Z= 0.166 Angle : 0.567 10.053 19391 Z= 0.289 Chirality : 0.039 0.165 2145 Planarity : 0.004 0.060 2478 Dihedral : 4.340 27.090 1885 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 0.65 % Allowed : 7.39 % Favored : 91.96 % 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: 0.74 (0.21), residues: 1708 helix: 1.32 (0.16), residues: 1088 sheet: 0.75 (0.55), residues: 96 loop : -1.31 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 775 HIS 0.003 0.001 HIS A2032 PHE 0.017 0.002 PHE A 720 TYR 0.027 0.001 TYR A1567 ARG 0.006 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 126 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.473 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 124 average time/residue: 0.2387 time to fit residues: 46.3369 Evaluate side-chains 113 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1296 time to fit residues: 2.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 149 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14335 Z= 0.168 Angle : 0.555 9.435 19391 Z= 0.285 Chirality : 0.039 0.155 2145 Planarity : 0.004 0.056 2478 Dihedral : 4.242 26.791 1885 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 0.72 % Allowed : 8.24 % Favored : 91.05 % 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: 0.81 (0.21), residues: 1708 helix: 1.37 (0.16), residues: 1089 sheet: 0.77 (0.55), residues: 96 loop : -1.26 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1247 HIS 0.004 0.001 HIS A2000 PHE 0.023 0.001 PHE A1690 TYR 0.025 0.001 TYR A1567 ARG 0.005 0.000 ARG A 662 *********************** 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 126 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.625 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 121 average time/residue: 0.2375 time to fit residues: 45.9501 Evaluate side-chains 116 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1448 time to fit residues: 3.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** A1014 HIS A1064 HIS A1371 HIS A1573 GLN A2351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1922 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= 0.246 Angle : 0.606 9.561 19391 Z= 0.309 Chirality : 0.040 0.160 2145 Planarity : 0.005 0.055 2478 Dihedral : 4.408 27.824 1885 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 0.65 % Allowed : 9.48 % Favored : 89.87 % 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: 1090 sheet: 0.68 (0.54), residues: 96 loop : -1.28 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1247 HIS 0.006 0.001 HIS A2000 PHE 0.022 0.002 PHE A 719 TYR 0.030 0.002 TYR A1567 ARG 0.008 0.001 ARG A 662 *********************** 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 124 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.596 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 121 average time/residue: 0.2522 time to fit residues: 47.2425 Evaluate side-chains 116 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1320 time to fit residues: 2.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 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: 0.7594 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14335 Z= 0.226 Angle : 0.592 10.465 19391 Z= 0.303 Chirality : 0.040 0.160 2145 Planarity : 0.004 0.054 2478 Dihedral : 4.440 28.795 1885 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 0.59 % Allowed : 10.00 % Favored : 89.41 % 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: 1.21 (0.16), residues: 1087 sheet: 0.75 (0.54), residues: 96 loop : -1.29 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1247 HIS 0.004 0.001 HIS A2000 PHE 0.030 0.002 PHE A1690 TYR 0.035 0.002 TYR A1567 ARG 0.005 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 127 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.598 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 123 average time/residue: 0.2487 time to fit residues: 47.7710 Evaluate side-chains 117 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1441 time to fit residues: 3.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 166 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.2207 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= 0.198 Angle : 0.587 11.453 19391 Z= 0.297 Chirality : 0.039 0.159 2145 Planarity : 0.004 0.054 2478 Dihedral : 4.407 28.536 1885 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 0.46 % Allowed : 10.78 % Favored : 88.76 % 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: 0.70 (0.21), residues: 1708 helix: 1.28 (0.16), residues: 1093 sheet: 0.73 (0.55), residues: 90 loop : -1.28 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1247 HIS 0.004 0.001 HIS A2000 PHE 0.028 0.002 PHE A1690 TYR 0.033 0.001 TYR A1567 ARG 0.004 0.000 ARG A 776 *********************** 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 126 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.700 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 123 average time/residue: 0.2457 time to fit residues: 47.6770 Evaluate side-chains 112 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1354 time to fit residues: 2.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 99 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14335 Z= 0.288 Angle : 0.644 13.232 19391 Z= 0.328 Chirality : 0.042 0.171 2145 Planarity : 0.005 0.056 2478 Dihedral : 4.605 29.416 1885 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.59 % Allowed : 10.92 % Favored : 88.50 % 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 (0.20), residues: 1708 helix: 1.08 (0.16), residues: 1091 sheet: 0.79 (0.56), residues: 90 loop : -1.25 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1247 HIS 0.006 0.001 HIS A2000 PHE 0.027 0.002 PHE A1690 TYR 0.038 0.002 TYR A1567 ARG 0.005 0.001 ARG A 822 *********************** 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 129 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.698 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 0.2708 time to fit residues: 52.4641 Evaluate side-chains 117 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1271 time to fit residues: 3.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14335 Z= 0.165 Angle : 0.585 12.038 19391 Z= 0.296 Chirality : 0.039 0.158 2145 Planarity : 0.004 0.056 2478 Dihedral : 4.418 28.584 1885 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 0.46 % Allowed : 11.44 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1708 helix: 1.30 (0.16), residues: 1091 sheet: 0.61 (0.55), residues: 91 loop : -1.21 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1247 HIS 0.003 0.001 HIS A2000 PHE 0.028 0.002 PHE A1690 TYR 0.034 0.001 TYR A1567 ARG 0.003 0.000 ARG A 544 *********************** 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 126 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.685 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 124 average time/residue: 0.2581 time to fit residues: 50.0372 Evaluate side-chains 113 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 172 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** A1573 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14335 Z= 0.176 Angle : 0.580 11.496 19391 Z= 0.295 Chirality : 0.039 0.159 2145 Planarity : 0.004 0.055 2478 Dihedral : 4.346 28.000 1885 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 0.33 % Allowed : 11.63 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1708 helix: 1.37 (0.16), residues: 1088 sheet: 0.67 (0.56), residues: 90 loop : -1.15 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1247 HIS 0.004 0.001 HIS A1932 PHE 0.030 0.002 PHE A1690 TYR 0.025 0.001 TYR A1567 ARG 0.003 0.000 ARG A 544 ********************** 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 122 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.758 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.2555 time to fit residues: 48.3987 Evaluate side-chains 118 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1409 time to fit residues: 2.8772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** A1573 GLN ** 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 = 0.4554 r_free = 0.4554 target = 0.195305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140008 restraints weight = 36039.824| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.23 r_work: 0.3612 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14335 Z= 0.215 Angle : 0.601 11.955 19391 Z= 0.306 Chirality : 0.040 0.161 2145 Planarity : 0.004 0.057 2478 Dihedral : 4.415 28.121 1885 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 0.39 % Allowed : 11.50 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1708 helix: 1.29 (0.16), residues: 1090 sheet: 0.58 (0.55), residues: 91 loop : -1.17 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1247 HIS 0.005 0.001 HIS A2000 PHE 0.038 0.002 PHE A1690 TYR 0.043 0.001 TYR A1567 ARG 0.004 0.000 ARG A 822 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.84 seconds wall clock time: 59 minutes 40.21 seconds (3580.21 seconds total)