Starting phenix.real_space_refine on Fri Feb 16 04:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj0_12368/02_2024/7nj0_12368_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 71 5.16 5 C 9167 2.51 5 N 2461 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ASP 887": "OD1" <-> "OD2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A ASP 1050": "OD1" <-> "OD2" Residue "A GLU 1115": "OE1" <-> "OE2" Residue "A PHE 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1382": "NH1" <-> "NH2" Residue "A ARG 1868": "NH1" <-> "NH2" Residue "A GLU 1875": "OE1" <-> "OE2" Residue "A GLU 1932": "OE1" <-> "OE2" Residue "A GLU 1972": "OE1" <-> "OE2" Residue "A ARG 2067": "NH1" <-> "NH2" Residue "A ARG 2101": "NH1" <-> "NH2" Residue "A ARG 2120": "NH1" <-> "NH2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14330 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9198 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 65, 'TRANS': 1122} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2349 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2173 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 610 Unusual residues: {'PO4': 1} Classifications: {'peptide': 70, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63, None: 1} Not linked: pdbres="PRO D 74 " pdbres="PO4 D 101 " Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG B 59 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 59 " occ=0.50 residue: pdb=" N GLN B 132 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN B 132 " occ=0.50 residue: pdb=" N TYR C 175 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR C 175 " occ=0.50 Time building chain proxies: 7.97, per 1000 atoms: 0.56 Number of scatterers: 14330 At special positions: 0 Unit cell: (91.52, 134.64, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 3 15.00 O 2628 8.00 N 2461 7.00 C 9167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 2.9 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 4 sheets defined 51.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 622 through 638 Processing helix chain 'A' and resid 649 through 662 removed outlier: 4.257A pdb=" N ILE A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 702 removed outlier: 4.381A pdb=" N GLN A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 737 through 758 removed outlier: 5.420A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 789 through 806 removed outlier: 4.334A pdb=" N GLU A 794 " --> pdb=" O MET A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 825 Processing helix chain 'A' and resid 832 through 845 removed outlier: 4.185A pdb=" N HIS A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 871 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.763A pdb=" N SER A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 Processing helix chain 'A' and resid 935 through 953 Processing helix chain 'A' and resid 976 through 998 removed outlier: 3.723A pdb=" N LYS A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1021 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 3.924A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1058 removed outlier: 3.714A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1154 through 1173 Processing helix chain 'A' and resid 1179 through 1206 Proline residue: A1192 - end of helix removed outlier: 3.638A pdb=" N ALA A1204 " --> pdb=" O GLN A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 4.077A pdb=" N ALA A1226 " --> pdb=" O ILE A1222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A1233 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1234 " --> pdb=" O LEU A1230 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1256 Processing helix chain 'A' and resid 1265 through 1277 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.704A pdb=" N SER A1290 " --> pdb=" O LEU A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1574 through 1588 removed outlier: 3.999A pdb=" N ALA A1584 " --> pdb=" O SER A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1607 removed outlier: 3.939A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 4.068A pdb=" N VAL A1620 " --> pdb=" O THR A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1644 removed outlier: 3.947A pdb=" N LEU A1632 " --> pdb=" O CYS A1628 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A1643 " --> pdb=" O GLN A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1677 Processing helix chain 'A' and resid 1688 through 1700 Processing helix chain 'A' and resid 1743 through 1745 No H-bonds generated for 'chain 'A' and resid 1743 through 1745' Processing helix chain 'A' and resid 1750 through 1767 Processing helix chain 'A' and resid 1773 through 1796 removed outlier: 3.612A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1805 removed outlier: 3.773A pdb=" N LYS A1803 " --> pdb=" O GLY A1800 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A1804 " --> pdb=" O CYS A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1827 removed outlier: 4.098A pdb=" N LEU A1825 " --> pdb=" O ARG A1821 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A1826 " --> pdb=" O LEU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1842 Processing helix chain 'A' and resid 1851 through 1861 Processing helix chain 'A' and resid 1868 through 1879 removed outlier: 3.625A pdb=" N GLU A1871 " --> pdb=" O ARG A1868 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1873 " --> pdb=" O GLN A1870 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN A1874 " --> pdb=" O GLU A1871 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1901 No H-bonds generated for 'chain 'A' and resid 1899 through 1901' Processing helix chain 'A' and resid 1904 through 1906 No H-bonds generated for 'chain 'A' and resid 1904 through 1906' Processing helix chain 'A' and resid 1922 through 1932 Processing helix chain 'A' and resid 1937 through 1940 No H-bonds generated for 'chain 'A' and resid 1937 through 1940' Processing helix chain 'A' and resid 1959 through 1971 removed outlier: 3.768A pdb=" N GLN A1964 " --> pdb=" O SER A1960 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A1968 " --> pdb=" O GLN A1964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1993 Processing helix chain 'A' and resid 2013 through 2017 Processing helix chain 'A' and resid 2045 through 2052 Processing helix chain 'A' and resid 2066 through 2083 removed outlier: 3.976A pdb=" N LEU A2081 " --> pdb=" O LEU A2077 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A2082 " --> pdb=" O GLN A2078 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2095 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 102 through 122 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 185 through 198 removed outlier: 3.661A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.382A pdb=" N ASN B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.517A pdb=" N TYR C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 216 Processing helix chain 'C' and resid 220 through 234 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.813A pdb=" N ALA C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.801A pdb=" N MET C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.581A pdb=" N ARG C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 removed outlier: 3.790A pdb=" N MET C 331 " --> pdb=" O MET C 327 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.893A pdb=" N LYS D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU D 31 " --> pdb=" O ASP D 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 26 through 31' Processing helix chain 'D' and resid 40 through 46 Processing sheet with id= A, first strand: chain 'A' and resid 1890 through 1895 removed outlier: 3.877A pdb=" N THR A1707 " --> pdb=" O HIS A1890 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1892 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A1724 " --> pdb=" O ALA A1714 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1948 through 1951 removed outlier: 6.779A pdb=" N LEU A1997 " --> pdb=" O PHE A1949 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL A1951 " --> pdb=" O LEU A1997 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A1999 " --> pdb=" O VAL A1951 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 77 through 81 removed outlier: 4.042A pdb=" N VAL B 18 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ARG B 22 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 6 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 17 through 23 606 hydrogen bonds defined for protein. 1794 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: 4.00 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4667 1.34 - 1.46: 3153 1.46 - 1.59: 6705 1.59 - 1.71: 7 1.71 - 1.83: 104 Bond restraints: 14636 Sorted by residual: bond pdb=" OG1 TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" O2P TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O3P TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3 PO4 D 101 " pdb=" P PO4 D 101 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" O4 PO4 D 101 " pdb=" P PO4 D 101 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.41e+00 ... (remaining 14631 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.43: 361 105.43 - 112.59: 7891 112.59 - 119.75: 4719 119.75 - 126.91: 6692 126.91 - 134.07: 216 Bond angle restraints: 19879 Sorted by residual: angle pdb=" C LEU A1129 " pdb=" CA LEU A1129 " pdb=" CB LEU A1129 " ideal model delta sigma weight residual 115.89 109.58 6.31 1.32e+00 5.74e-01 2.28e+01 angle pdb=" N GLY A1814 " pdb=" CA GLY A1814 " pdb=" C GLY A1814 " ideal model delta sigma weight residual 112.34 120.35 -8.01 2.04e+00 2.40e-01 1.54e+01 angle pdb=" CB TPO B 161 " pdb=" OG1 TPO B 161 " pdb=" P TPO B 161 " ideal model delta sigma weight residual 119.31 107.64 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C CYS C 167 " pdb=" N SER C 168 " pdb=" CA SER C 168 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 angle pdb=" CA GLY A1744 " pdb=" C GLY A1744 " pdb=" O GLY A1744 " ideal model delta sigma weight residual 120.75 117.40 3.35 1.03e+00 9.43e-01 1.06e+01 ... (remaining 19874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 8029 16.97 - 33.93: 728 33.93 - 50.90: 106 50.90 - 67.87: 23 67.87 - 84.83: 10 Dihedral angle restraints: 8896 sinusoidal: 3579 harmonic: 5317 Sorted by residual: dihedral pdb=" CA GLY A 955 " pdb=" C GLY A 955 " pdb=" N SER A 956 " pdb=" CA SER A 956 " ideal model delta harmonic sigma weight residual 180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ILE B 155 " pdb=" C ILE B 155 " pdb=" N PRO B 156 " pdb=" CA PRO B 156 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE A2050 " pdb=" C ILE A2050 " pdb=" N MET A2051 " pdb=" CA MET A2051 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 8893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1286 0.028 - 0.057: 675 0.057 - 0.085: 218 0.085 - 0.114: 88 0.114 - 0.142: 18 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CB ILE B 10 " pdb=" CA ILE B 10 " pdb=" CG1 ILE B 10 " pdb=" CG2 ILE B 10 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASP A1050 " pdb=" N ASP A1050 " pdb=" C ASP A1050 " pdb=" CB ASP A1050 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO A1919 " pdb=" N PRO A1919 " pdb=" C PRO A1919 " pdb=" CB PRO A1919 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 2282 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 183 " -0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO B 184 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 184 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 184 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2113 " -0.010 2.00e-02 2.50e+03 1.40e-02 3.95e+00 pdb=" CG TYR A2113 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A2113 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A2113 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A2113 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A2113 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A2113 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A2113 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 155 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 156 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " -0.026 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1181 2.74 - 3.28: 14644 3.28 - 3.82: 22546 3.82 - 4.36: 26834 4.36 - 4.90: 46538 Nonbonded interactions: 111743 Sorted by model distance: nonbonded pdb=" O MET C 327 " pdb=" OG1 THR C 330 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASN A1236 " pdb=" NE2 GLN A1717 " model vdw 2.209 2.520 nonbonded pdb=" OD1 ASP B 101 " pdb=" OG SER B 103 " model vdw 2.233 2.440 nonbonded pdb=" OG SER A1625 " pdb=" OG SER A1920 " model vdw 2.242 2.440 nonbonded pdb=" NH2 ARG A1586 " pdb=" O HIS A1686 " model vdw 2.263 2.520 ... (remaining 111738 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.150 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: 0.000 Extract box with map and model: 9.670 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.980 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.005 0.115 14636 Z= 0.293 Angle : 0.661 11.669 19879 Z= 0.352 Chirality : 0.040 0.142 2285 Planarity : 0.005 0.074 2526 Dihedral : 13.213 84.834 5443 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.18), residues: 1792 helix: -1.10 (0.15), residues: 985 sheet: -2.54 (0.45), residues: 99 loop : -2.82 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 244 HIS 0.004 0.001 HIS A1630 PHE 0.016 0.001 PHE A1100 TYR 0.033 0.001 TYR A2113 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.644 Fit side-chains REVERT: A 700 ASP cc_start: 0.8097 (t0) cc_final: 0.7825 (m-30) REVERT: A 762 GLN cc_start: 0.5885 (mt0) cc_final: 0.5498 (pt0) REVERT: A 948 SER cc_start: 0.8182 (m) cc_final: 0.7919 (t) REVERT: A 1817 GLN cc_start: 0.6600 (tp40) cc_final: 0.6227 (pt0) REVERT: A 1840 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7439 (tppt) REVERT: A 1920 SER cc_start: 0.8573 (m) cc_final: 0.8287 (t) REVERT: A 1990 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 1994 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7207 (mmtp) REVERT: A 2074 GLU cc_start: 0.8648 (tp30) cc_final: 0.8115 (tp30) REVERT: B 8 GLU cc_start: 0.7068 (pt0) cc_final: 0.6395 (pm20) REVERT: B 34 LYS cc_start: 0.7725 (tttp) cc_final: 0.7157 (tmtt) REVERT: B 77 TYR cc_start: 0.7048 (m-80) cc_final: 0.6791 (m-80) REVERT: B 136 ILE cc_start: 0.9107 (pt) cc_final: 0.8682 (mt) REVERT: B 269 ILE cc_start: 0.8023 (mm) cc_final: 0.7804 (mt) REVERT: C 328 GLU cc_start: 0.8115 (tp30) cc_final: 0.7524 (tp30) REVERT: D 23 MET cc_start: 0.7702 (mtp) cc_final: 0.7327 (mtm) REVERT: D 45 ASN cc_start: 0.6692 (t0) cc_final: 0.6380 (m-40) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3078 time to fit residues: 131.7318 Evaluate side-chains 172 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A 821 GLN A1200 GLN A1761 GLN A1827 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN C 367 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14636 Z= 0.219 Angle : 0.605 8.576 19879 Z= 0.295 Chirality : 0.039 0.143 2285 Planarity : 0.004 0.065 2526 Dihedral : 4.952 58.504 1960 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.59 % Allowed : 10.52 % Favored : 87.89 % 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: -1.41 (0.20), residues: 1792 helix: 0.09 (0.16), residues: 996 sheet: -2.12 (0.48), residues: 96 loop : -2.26 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 54 HIS 0.008 0.001 HIS C 367 PHE 0.015 0.001 PHE A1100 TYR 0.017 0.001 TYR A2113 ARG 0.006 0.000 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8128 (t0) cc_final: 0.7778 (m-30) REVERT: A 762 GLN cc_start: 0.5866 (mt0) cc_final: 0.5384 (pt0) REVERT: A 907 LEU cc_start: 0.8920 (tp) cc_final: 0.8657 (tp) REVERT: A 948 SER cc_start: 0.8139 (m) cc_final: 0.7847 (t) REVERT: A 1817 GLN cc_start: 0.6672 (tp40) cc_final: 0.6183 (pt0) REVERT: A 1840 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7545 (tppt) REVERT: A 1920 SER cc_start: 0.8546 (m) cc_final: 0.8279 (t) REVERT: A 1933 TYR cc_start: 0.6969 (m-80) cc_final: 0.6257 (m-10) REVERT: A 1990 GLU cc_start: 0.6404 (mt-10) cc_final: 0.6181 (mt-10) REVERT: A 2074 GLU cc_start: 0.8615 (tp30) cc_final: 0.8097 (tp30) REVERT: A 2095 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 34 LYS cc_start: 0.7551 (tttp) cc_final: 0.7073 (tmtt) REVERT: B 77 TYR cc_start: 0.7064 (m-80) cc_final: 0.6855 (m-80) REVERT: B 98 GLN cc_start: 0.7840 (mt0) cc_final: 0.7612 (mt0) REVERT: B 136 ILE cc_start: 0.9124 (pt) cc_final: 0.8683 (mt) REVERT: B 180 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8547 (mtp180) REVERT: B 237 TYR cc_start: 0.7393 (t80) cc_final: 0.7109 (t80) REVERT: C 328 GLU cc_start: 0.8017 (tp30) cc_final: 0.7432 (tp30) REVERT: C 336 MET cc_start: 0.8456 (ptp) cc_final: 0.8032 (ttp) REVERT: D 23 MET cc_start: 0.7967 (mtp) cc_final: 0.7444 (mtm) outliers start: 25 outliers final: 17 residues processed: 214 average time/residue: 0.2636 time to fit residues: 84.8173 Evaluate side-chains 189 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 0.0030 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 0.0040 chunk 177 optimal weight: 0.0270 chunk 146 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 871 HIS A1674 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS B 126 HIS B 132 GLN D 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14636 Z= 0.143 Angle : 0.511 8.755 19879 Z= 0.250 Chirality : 0.037 0.127 2285 Planarity : 0.004 0.066 2526 Dihedral : 4.501 57.212 1960 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.04 % Allowed : 11.92 % Favored : 86.04 % 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: -0.51 (0.21), residues: 1792 helix: 0.84 (0.17), residues: 987 sheet: -1.20 (0.53), residues: 93 loop : -1.94 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 54 HIS 0.002 0.000 HIS A 809 PHE 0.013 0.001 PHE A1100 TYR 0.009 0.001 TYR B 181 ARG 0.003 0.000 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8109 (t0) cc_final: 0.7682 (m-30) REVERT: A 762 GLN cc_start: 0.5790 (mt0) cc_final: 0.5391 (pt0) REVERT: A 948 SER cc_start: 0.8109 (m) cc_final: 0.7832 (t) REVERT: A 1050 ASP cc_start: 0.8074 (m-30) cc_final: 0.7841 (m-30) REVERT: A 1812 GLU cc_start: 0.6516 (tp30) cc_final: 0.6298 (tt0) REVERT: A 1817 GLN cc_start: 0.6748 (tp40) cc_final: 0.6230 (pt0) REVERT: A 1840 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7444 (tppt) REVERT: A 1933 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6320 (m-10) REVERT: A 2074 GLU cc_start: 0.8610 (tp30) cc_final: 0.8085 (tp30) REVERT: B 34 LYS cc_start: 0.7714 (tttp) cc_final: 0.7297 (tmtt) REVERT: B 136 ILE cc_start: 0.9192 (pt) cc_final: 0.8756 (mt) REVERT: D 23 MET cc_start: 0.7891 (mtp) cc_final: 0.7354 (mtm) outliers start: 32 outliers final: 19 residues processed: 218 average time/residue: 0.2485 time to fit residues: 82.7277 Evaluate side-chains 187 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 47 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN C 319 GLN C 367 HIS D 45 ASN D 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14636 Z= 0.169 Angle : 0.510 8.664 19879 Z= 0.248 Chirality : 0.037 0.122 2285 Planarity : 0.004 0.067 2526 Dihedral : 4.358 56.129 1960 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 2.49 % Allowed : 13.51 % Favored : 84.00 % 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: -0.16 (0.21), residues: 1792 helix: 1.11 (0.17), residues: 987 sheet: -1.03 (0.54), residues: 93 loop : -1.76 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.009 0.001 HIS C 367 PHE 0.014 0.001 PHE A1100 TYR 0.013 0.001 TYR A 685 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.652 Fit side-chains revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8189 (t0) cc_final: 0.7721 (m-30) REVERT: A 762 GLN cc_start: 0.5677 (mt0) cc_final: 0.5349 (pt0) REVERT: A 948 SER cc_start: 0.8117 (m) cc_final: 0.7837 (t) REVERT: A 997 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7293 (t-90) REVERT: A 1050 ASP cc_start: 0.8129 (m-30) cc_final: 0.7796 (m-30) REVERT: A 1382 ARG cc_start: 0.6334 (ptt180) cc_final: 0.5598 (ptp90) REVERT: A 1817 GLN cc_start: 0.6627 (tp40) cc_final: 0.6317 (pt0) REVERT: A 1840 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7475 (tppt) REVERT: A 1933 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: A 2074 GLU cc_start: 0.8603 (tp30) cc_final: 0.8065 (tp30) REVERT: B 34 LYS cc_start: 0.7902 (tttp) cc_final: 0.7468 (tmtt) REVERT: B 136 ILE cc_start: 0.9025 (pt) cc_final: 0.8658 (mt) REVERT: C 288 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8153 (ttpp) REVERT: C 328 GLU cc_start: 0.7904 (tp30) cc_final: 0.7340 (tp30) REVERT: D 23 MET cc_start: 0.7900 (mtp) cc_final: 0.7361 (mtm) REVERT: D 70 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.5939 (ttm170) outliers start: 39 outliers final: 24 residues processed: 201 average time/residue: 0.2515 time to fit residues: 77.0210 Evaluate side-chains 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1789 VAL Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.0770 chunk 157 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 132 GLN C 319 GLN D 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14636 Z= 0.175 Angle : 0.509 9.054 19879 Z= 0.246 Chirality : 0.037 0.123 2285 Planarity : 0.004 0.066 2526 Dihedral : 4.300 55.463 1960 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 2.61 % Allowed : 13.96 % Favored : 83.43 % 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: 0.06 (0.21), residues: 1792 helix: 1.26 (0.17), residues: 990 sheet: -0.95 (0.54), residues: 93 loop : -1.61 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 43 HIS 0.003 0.001 HIS A1630 PHE 0.014 0.001 PHE A1100 TYR 0.012 0.001 TYR A 685 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8249 (t0) cc_final: 0.7717 (m-30) REVERT: A 762 GLN cc_start: 0.5573 (mt0) cc_final: 0.5325 (pt0) REVERT: A 783 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: A 948 SER cc_start: 0.8117 (m) cc_final: 0.7819 (t) REVERT: A 997 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7311 (t-90) REVERT: A 1050 ASP cc_start: 0.8160 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1382 ARG cc_start: 0.6320 (ptt180) cc_final: 0.5579 (ptp90) REVERT: A 1817 GLN cc_start: 0.6705 (tp40) cc_final: 0.6381 (pt0) REVERT: A 1840 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7438 (tppt) REVERT: A 1933 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6542 (m-10) REVERT: A 2074 GLU cc_start: 0.8611 (tp30) cc_final: 0.8054 (tp30) REVERT: B 34 LYS cc_start: 0.7875 (tttp) cc_final: 0.7485 (tmtt) REVERT: B 136 ILE cc_start: 0.8999 (pt) cc_final: 0.8679 (mt) REVERT: C 288 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (ttpp) REVERT: C 328 GLU cc_start: 0.7937 (tp30) cc_final: 0.7365 (tp30) REVERT: D 23 MET cc_start: 0.7905 (mtp) cc_final: 0.7331 (mtm) REVERT: D 70 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5921 (ttm170) outliers start: 41 outliers final: 27 residues processed: 197 average time/residue: 0.2510 time to fit residues: 75.4475 Evaluate side-chains 197 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1789 VAL Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 0.0970 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 ASN A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14636 Z= 0.148 Angle : 0.493 8.595 19879 Z= 0.239 Chirality : 0.036 0.146 2285 Planarity : 0.004 0.063 2526 Dihedral : 4.178 55.403 1960 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 2.42 % Allowed : 14.34 % Favored : 83.24 % 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: 0.33 (0.21), residues: 1792 helix: 1.47 (0.17), residues: 995 sheet: -0.81 (0.55), residues: 88 loop : -1.51 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 43 HIS 0.010 0.001 HIS C 367 PHE 0.013 0.001 PHE A1100 TYR 0.014 0.001 TYR A 685 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8246 (t0) cc_final: 0.7709 (m-30) REVERT: A 762 GLN cc_start: 0.5609 (mt0) cc_final: 0.5405 (pt0) REVERT: A 783 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 948 SER cc_start: 0.8130 (m) cc_final: 0.7827 (t) REVERT: A 997 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7330 (t-90) REVERT: A 1038 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 1050 ASP cc_start: 0.8156 (m-30) cc_final: 0.7792 (m-30) REVERT: A 1382 ARG cc_start: 0.6264 (ptt180) cc_final: 0.5563 (ptp90) REVERT: A 1817 GLN cc_start: 0.6686 (tp40) cc_final: 0.6359 (pt0) REVERT: A 1821 ARG cc_start: 0.7881 (tmt-80) cc_final: 0.7632 (ptm160) REVERT: A 1840 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7426 (tppt) REVERT: A 1899 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 1933 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: A 2074 GLU cc_start: 0.8639 (tp30) cc_final: 0.8064 (tp30) REVERT: B 34 LYS cc_start: 0.7871 (tttp) cc_final: 0.7476 (tmtt) REVERT: B 98 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: B 136 ILE cc_start: 0.8953 (pt) cc_final: 0.8734 (mt) REVERT: C 288 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8119 (ttpp) REVERT: C 328 GLU cc_start: 0.7935 (tp30) cc_final: 0.7381 (tp30) REVERT: D 23 MET cc_start: 0.7907 (mtp) cc_final: 0.7347 (mtm) REVERT: D 58 MET cc_start: 0.7629 (ptm) cc_final: 0.7029 (ptp) REVERT: D 70 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.5891 (ttm170) outliers start: 38 outliers final: 27 residues processed: 198 average time/residue: 0.2485 time to fit residues: 74.3295 Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14636 Z= 0.186 Angle : 0.509 7.660 19879 Z= 0.247 Chirality : 0.037 0.137 2285 Planarity : 0.004 0.067 2526 Dihedral : 4.187 54.393 1960 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 2.74 % Allowed : 13.83 % Favored : 83.43 % 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: 0.35 (0.21), residues: 1792 helix: 1.48 (0.17), residues: 999 sheet: -0.83 (0.58), residues: 81 loop : -1.48 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 54 HIS 0.004 0.001 HIS A1630 PHE 0.013 0.001 PHE A1100 TYR 0.012 0.001 TYR A 685 ARG 0.003 0.000 ARG A1629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8244 (t0) cc_final: 0.7722 (m-30) REVERT: A 783 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: A 948 SER cc_start: 0.8067 (m) cc_final: 0.7826 (t) REVERT: A 997 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: A 1038 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 1050 ASP cc_start: 0.8199 (m-30) cc_final: 0.7982 (m-30) REVERT: A 1382 ARG cc_start: 0.6318 (ptt180) cc_final: 0.5664 (ptp90) REVERT: A 1817 GLN cc_start: 0.6741 (tp40) cc_final: 0.6450 (pt0) REVERT: A 1821 ARG cc_start: 0.7918 (tmt-80) cc_final: 0.7680 (ptm160) REVERT: A 1840 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7359 (ttmt) REVERT: A 1899 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 1933 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6584 (m-10) REVERT: A 2074 GLU cc_start: 0.8632 (tp30) cc_final: 0.8061 (tp30) REVERT: B 34 LYS cc_start: 0.7813 (tttp) cc_final: 0.7431 (tmtt) REVERT: B 98 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: B 136 ILE cc_start: 0.8986 (pt) cc_final: 0.8772 (mt) REVERT: C 288 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: C 328 GLU cc_start: 0.7963 (tp30) cc_final: 0.7375 (tp30) REVERT: D 23 MET cc_start: 0.7944 (mtp) cc_final: 0.7388 (mtm) REVERT: D 58 MET cc_start: 0.7681 (ptm) cc_final: 0.7066 (ptp) REVERT: D 70 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.5923 (ttm170) outliers start: 43 outliers final: 31 residues processed: 195 average time/residue: 0.2583 time to fit residues: 76.1523 Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1789 VAL Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14636 Z= 0.151 Angle : 0.489 6.803 19879 Z= 0.238 Chirality : 0.036 0.127 2285 Planarity : 0.004 0.063 2526 Dihedral : 4.108 54.351 1960 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.31 % Rotamer: Outliers : 2.74 % Allowed : 14.28 % Favored : 82.98 % 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: 0.54 (0.21), residues: 1792 helix: 1.62 (0.17), residues: 996 sheet: -0.73 (0.58), residues: 81 loop : -1.37 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 54 HIS 0.002 0.000 HIS B 126 PHE 0.016 0.001 PHE A1757 TYR 0.014 0.001 TYR A 685 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 700 ASP cc_start: 0.8251 (t0) cc_final: 0.7708 (m-30) REVERT: A 783 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: A 948 SER cc_start: 0.8080 (m) cc_final: 0.7850 (t) REVERT: A 997 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7357 (t-90) REVERT: A 1038 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 1050 ASP cc_start: 0.8187 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1382 ARG cc_start: 0.6352 (ptt180) cc_final: 0.5682 (ptp90) REVERT: A 1727 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 1817 GLN cc_start: 0.6741 (tp40) cc_final: 0.6362 (pt0) REVERT: A 1821 ARG cc_start: 0.7918 (tmt-80) cc_final: 0.7698 (ptm160) REVERT: A 1933 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: A 2074 GLU cc_start: 0.8634 (tp30) cc_final: 0.8053 (tp30) REVERT: B 34 LYS cc_start: 0.7805 (tttp) cc_final: 0.7419 (tmtt) REVERT: B 98 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: C 328 GLU cc_start: 0.7953 (tp30) cc_final: 0.7391 (tp30) REVERT: C 336 MET cc_start: 0.8082 (ptp) cc_final: 0.7578 (ttp) REVERT: D 23 MET cc_start: 0.7903 (mtp) cc_final: 0.7380 (mtm) REVERT: D 42 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7697 (mt-10) REVERT: D 58 MET cc_start: 0.7669 (ptm) cc_final: 0.7060 (ptp) REVERT: D 70 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.5912 (ttm170) outliers start: 43 outliers final: 29 residues processed: 199 average time/residue: 0.2461 time to fit residues: 75.0049 Evaluate side-chains 202 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14636 Z= 0.167 Angle : 0.494 6.780 19879 Z= 0.241 Chirality : 0.037 0.131 2285 Planarity : 0.004 0.065 2526 Dihedral : 4.079 53.428 1960 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 2.36 % Allowed : 14.72 % Favored : 82.92 % 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: 0.55 (0.21), residues: 1792 helix: 1.62 (0.17), residues: 1000 sheet: -1.04 (0.56), residues: 81 loop : -1.33 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 54 HIS 0.003 0.001 HIS A1630 PHE 0.015 0.001 PHE A1757 TYR 0.013 0.001 TYR A 685 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.741 Fit side-chains REVERT: A 700 ASP cc_start: 0.8237 (t0) cc_final: 0.7915 (m-30) REVERT: A 783 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: A 948 SER cc_start: 0.8105 (m) cc_final: 0.7869 (t) REVERT: A 997 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: A 1038 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 1050 ASP cc_start: 0.8225 (m-30) cc_final: 0.7877 (m-30) REVERT: A 1382 ARG cc_start: 0.6344 (ptt180) cc_final: 0.5696 (ptp90) REVERT: A 1727 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 1817 GLN cc_start: 0.6719 (tp40) cc_final: 0.6339 (pt0) REVERT: A 1821 ARG cc_start: 0.7916 (tmt-80) cc_final: 0.7686 (ptm160) REVERT: A 1933 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: A 2074 GLU cc_start: 0.8623 (tp30) cc_final: 0.8047 (tp30) REVERT: B 34 LYS cc_start: 0.7807 (tttp) cc_final: 0.7440 (tmtt) REVERT: B 98 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: B 141 THR cc_start: 0.8214 (m) cc_final: 0.7907 (p) REVERT: C 328 GLU cc_start: 0.7962 (tp30) cc_final: 0.7430 (tp30) REVERT: D 23 MET cc_start: 0.7904 (mtp) cc_final: 0.7357 (mtm) REVERT: D 58 MET cc_start: 0.7728 (ptm) cc_final: 0.7138 (ptp) REVERT: D 70 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.5977 (ttm170) outliers start: 37 outliers final: 28 residues processed: 195 average time/residue: 0.2517 time to fit residues: 75.6092 Evaluate side-chains 198 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 14 optimal weight: 0.0370 chunk 110 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14636 Z= 0.162 Angle : 0.495 7.184 19879 Z= 0.240 Chirality : 0.036 0.128 2285 Planarity : 0.004 0.063 2526 Dihedral : 4.048 52.316 1960 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 2.29 % Allowed : 15.23 % Favored : 82.47 % 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: 1792 helix: 1.66 (0.17), residues: 997 sheet: -0.60 (0.53), residues: 89 loop : -1.28 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 54 HIS 0.002 0.001 HIS B 126 PHE 0.013 0.001 PHE A1757 TYR 0.017 0.001 TYR B 90 ARG 0.003 0.000 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.545 Fit side-chains REVERT: A 700 ASP cc_start: 0.8214 (t0) cc_final: 0.7876 (m-30) REVERT: A 783 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: A 948 SER cc_start: 0.8113 (m) cc_final: 0.7878 (t) REVERT: A 997 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7416 (t-90) REVERT: A 1038 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 1050 ASP cc_start: 0.8230 (m-30) cc_final: 0.7885 (m-30) REVERT: A 1382 ARG cc_start: 0.6288 (ptt180) cc_final: 0.5669 (ptp90) REVERT: A 1727 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 1817 GLN cc_start: 0.6816 (tp40) cc_final: 0.6394 (pt0) REVERT: A 1821 ARG cc_start: 0.7910 (tmt-80) cc_final: 0.7693 (ptm160) REVERT: A 1933 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: A 2074 GLU cc_start: 0.8625 (tp30) cc_final: 0.8035 (tp30) REVERT: B 34 LYS cc_start: 0.7808 (tttp) cc_final: 0.7403 (tmtt) REVERT: B 98 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: B 141 THR cc_start: 0.8184 (m) cc_final: 0.7918 (p) REVERT: B 230 GLU cc_start: 0.6435 (tt0) cc_final: 0.6203 (tm-30) REVERT: C 328 GLU cc_start: 0.7918 (tp30) cc_final: 0.7338 (tp30) REVERT: C 336 MET cc_start: 0.8115 (ptp) cc_final: 0.7667 (ttp) REVERT: D 23 MET cc_start: 0.7895 (mtp) cc_final: 0.7365 (mtm) REVERT: D 42 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7698 (mt-10) REVERT: D 58 MET cc_start: 0.7723 (ptm) cc_final: 0.7097 (ptp) REVERT: D 70 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.5945 (ttm170) outliers start: 36 outliers final: 30 residues processed: 188 average time/residue: 0.2567 time to fit residues: 74.2943 Evaluate side-chains 197 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1933 TYR Chi-restraints excluded: chain A residue 1957 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 60 optimal weight: 0.0060 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142332 restraints weight = 19376.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144306 restraints weight = 13969.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145355 restraints weight = 11088.690| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14636 Z= 0.169 Angle : 0.497 6.662 19879 Z= 0.242 Chirality : 0.037 0.128 2285 Planarity : 0.004 0.064 2526 Dihedral : 4.019 49.824 1960 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 2.55 % Allowed : 15.36 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1792 helix: 1.70 (0.17), residues: 998 sheet: -0.62 (0.53), residues: 89 loop : -1.31 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 54 HIS 0.011 0.001 HIS C 367 PHE 0.013 0.001 PHE A1100 TYR 0.018 0.001 TYR B 90 ARG 0.003 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.69 seconds wall clock time: 53 minutes 22.82 seconds (3202.82 seconds total)