Starting phenix.real_space_refine on Sun Feb 18 05:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/02_2024/6x9o_22106.pdb" } resolution = 2.6 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= 0.004 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 130 5.16 5 C 13379 2.51 5 N 3603 2.21 5 O 3787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A GLU 820": "OE1" <-> "OE2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A ARG 987": "NH1" <-> "NH2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A GLU 1029": "OE1" <-> "OE2" Residue "A GLU 1293": "OE1" <-> "OE2" Residue "A GLU 1294": "OE1" <-> "OE2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A GLU 1306": "OE1" <-> "OE2" Residue "A ARG 1425": "NH1" <-> "NH2" Residue "A GLU 1491": "OE1" <-> "OE2" Residue "A GLU 1509": "OE1" <-> "OE2" Residue "A GLU 1567": "OE1" <-> "OE2" Residue "A ARG 1579": "NH1" <-> "NH2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A GLU 1631": "OE1" <-> "OE2" Residue "A ARG 1683": "NH1" <-> "NH2" Residue "A ARG 1697": "NH1" <-> "NH2" Residue "A ARG 1715": "NH1" <-> "NH2" Residue "A GLU 1739": "OE1" <-> "OE2" Residue "A ARG 1744": "NH1" <-> "NH2" Residue "A GLU 1765": "OE1" <-> "OE2" Residue "A ARG 1795": "NH1" <-> "NH2" Residue "A ARG 1806": "NH1" <-> "NH2" Residue "A ARG 1823": "NH1" <-> "NH2" Residue "A ARG 1897": "NH1" <-> "NH2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A ARG 1997": "NH1" <-> "NH2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A GLU 2019": "OE1" <-> "OE2" Residue "A ARG 2065": "NH1" <-> "NH2" Residue "A GLU 2172": "OE1" <-> "OE2" Residue "A GLU 2370": "OE1" <-> "OE2" Residue "A ARG 2395": "NH1" <-> "NH2" Residue "A ARG 2403": "NH1" <-> "NH2" Residue "A ARG 2412": "NH1" <-> "NH2" Residue "A GLU 2446": "OE1" <-> "OE2" Residue "A ARG 2463": "NH1" <-> "NH2" Residue "A ARG 2553": "NH1" <-> "NH2" Residue "A GLU 2557": "OE1" <-> "OE2" Residue "A GLU 2568": "OE1" <-> "OE2" Residue "A ARG 2665": "NH1" <-> "NH2" Residue "A ARG 2704": "NH1" <-> "NH2" Residue "A GLU 2715": "OE1" <-> "OE2" Residue "A GLU 2720": "OE1" <-> "OE2" Residue "A GLU 2728": "OE1" <-> "OE2" Residue "A ARG 2731": "NH1" <-> "NH2" Residue "A GLU 2738": "OE1" <-> "OE2" Residue "A GLU 2870": "OE1" <-> "OE2" Residue "A GLU 2885": "OE1" <-> "OE2" Residue "A ARG 2908": "NH1" <-> "NH2" Residue "A ARG 2916": "NH1" <-> "NH2" Residue "A GLU 2974": "OE1" <-> "OE2" Residue "A GLU 3002": "OE1" <-> "OE2" Residue "A ARG 3048": "NH1" <-> "NH2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20899 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2425, 19063 Classifications: {'peptide': 2425} Link IDs: {'PTRANS': 109, 'TRANS': 2315} Chain breaks: 18 Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1836 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 15, 'TRANS': 228} Chain breaks: 2 Time building chain proxies: 11.16, per 1000 atoms: 0.53 Number of scatterers: 20899 At special positions: 0 Unit cell: (139.74, 151.248, 123.3, 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 130 16.00 O 3787 8.00 N 3603 7.00 C 13379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.07 Simple disulfide: pdb=" SG CYS A 774 " - pdb=" SG CYS A 809 " distance=2.05 Simple disulfide: pdb=" SG CYS A1049 " - pdb=" SG CYS A1064 " 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: 8.53 Conformation dependent library (CDL) restraints added in 3.9 seconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 98 through 112 removed outlier: 4.910A pdb=" N CYS A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.932A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.839A pdb=" N ASP A 140 " --> pdb=" O CYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 removed outlier: 4.094A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 Proline residue: A 166 - end of helix removed outlier: 3.558A pdb=" N GLU A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 203 through 220 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 223 through 242 Proline residue: A 235 - end of helix removed outlier: 3.641A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.649A pdb=" N ALA A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 352 through 367 Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.677A pdb=" N GLN A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.615A pdb=" N GLY A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.840A pdb=" N HIS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 728 removed outlier: 3.747A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.685A pdb=" N ASP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 785 Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 805 through 808 Processing helix chain 'A' and resid 809 through 818 Processing helix chain 'A' and resid 821 through 841 removed outlier: 5.249A pdb=" N MET A 837 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 removed outlier: 3.637A pdb=" N LEU A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 861 removed outlier: 3.615A pdb=" N ASN A 860 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 876 removed outlier: 3.607A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 889 Processing helix chain 'A' and resid 895 through 899 removed outlier: 4.197A pdb=" N HIS A 898 " --> pdb=" O GLY A 895 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 899 " --> pdb=" O ALA A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 899' Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 937 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 950 through 964 removed outlier: 4.121A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 963 " --> pdb=" O GLN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1017 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1066 through 1077 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1101 Processing helix chain 'A' and resid 1102 through 1106 removed outlier: 4.131A pdb=" N LYS A1105 " --> pdb=" O SER A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1159 Processing helix chain 'A' and resid 1235 through 1253 Processing helix chain 'A' and resid 1263 through 1280 Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1291 through 1303 removed outlier: 3.676A pdb=" N SER A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1361 through 1375 Processing helix chain 'A' and resid 1376 through 1377 No H-bonds generated for 'chain 'A' and resid 1376 through 1377' Processing helix chain 'A' and resid 1423 through 1426 Processing helix chain 'A' and resid 1427 through 1441 Processing helix chain 'A' and resid 1443 through 1460 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.891A pdb=" N LEU A1467 " --> pdb=" O ASN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1487 removed outlier: 3.687A pdb=" N PHE A1481 " --> pdb=" O VAL A1477 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A1482 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A1483 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1509 removed outlier: 3.680A pdb=" N TYR A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1532 Processing helix chain 'A' and resid 1539 through 1553 Proline residue: A1546 - end of helix Processing helix chain 'A' and resid 1564 through 1580 removed outlier: 3.668A pdb=" N THR A1568 " --> pdb=" O LYS A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1601 removed outlier: 3.874A pdb=" N LYS A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1623 removed outlier: 3.556A pdb=" N ILE A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Proline residue: A1618 - end of helix Processing helix chain 'A' and resid 1629 through 1643 Processing helix chain 'A' and resid 1644 through 1649 Processing helix chain 'A' and resid 1651 through 1659 Processing helix chain 'A' and resid 1667 through 1689 Processing helix chain 'A' and resid 1690 through 1701 Processing helix chain 'A' and resid 1704 through 1708 removed outlier: 3.998A pdb=" N ILE A1708 " --> pdb=" O PRO A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1718 removed outlier: 3.764A pdb=" N ASP A1718 " --> pdb=" O ASN A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1759 Processing helix chain 'A' and resid 1767 through 1791 Processing helix chain 'A' and resid 1794 through 1806 removed outlier: 3.544A pdb=" N ARG A1806 " --> pdb=" O THR A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1826 removed outlier: 3.638A pdb=" N SER A1826 " --> pdb=" O LEU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1831 through 1845 Processing helix chain 'A' and resid 1852 through 1857 Processing helix chain 'A' and resid 1890 through 1911 removed outlier: 3.615A pdb=" N GLN A1910 " --> pdb=" O ASP A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1932 removed outlier: 7.032A pdb=" N GLN A1927 " --> pdb=" O VAL A1923 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP A1928 " --> pdb=" O ASN A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1947 Processing helix chain 'A' and resid 1948 through 1961 Processing helix chain 'A' and resid 1968 through 1981 removed outlier: 4.632A pdb=" N GLY A1981 " --> pdb=" O GLN A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1987 Processing helix chain 'A' and resid 1988 through 1997 Processing helix chain 'A' and resid 2003 through 2024 Processing helix chain 'A' and resid 2025 through 2033 removed outlier: 3.873A pdb=" N ALA A2031 " --> pdb=" O GLN A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2048 removed outlier: 3.598A pdb=" N LEU A2038 " --> pdb=" O PRO A2034 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A2039 " --> pdb=" O MET A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2054 removed outlier: 3.634A pdb=" N ARG A2053 " --> pdb=" O GLY A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2069 removed outlier: 3.677A pdb=" N TYR A2058 " --> pdb=" O HIS A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2111 removed outlier: 3.626A pdb=" N GLN A2109 " --> pdb=" O LEU A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2126 Processing helix chain 'A' and resid 2129 through 2133 removed outlier: 3.659A pdb=" N MET A2133 " --> pdb=" O ALA A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2145 No H-bonds generated for 'chain 'A' and resid 2143 through 2145' Processing helix chain 'A' and resid 2146 through 2159 Processing helix chain 'A' and resid 2164 through 2184 removed outlier: 3.639A pdb=" N GLN A2184 " --> pdb=" O GLY A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2211 removed outlier: 3.961A pdb=" N PHE A2211 " --> pdb=" O LEU A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2216 through 2218 No H-bonds generated for 'chain 'A' and resid 2216 through 2218' Processing helix chain 'A' and resid 2219 through 2232 removed outlier: 3.607A pdb=" N ALA A2226 " --> pdb=" O THR A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2237 removed outlier: 3.875A pdb=" N LEU A2237 " --> pdb=" O VAL A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2242 Processing helix chain 'A' and resid 2246 through 2269 removed outlier: 4.620A pdb=" N ASP A2250 " --> pdb=" O GLU A2246 " (cutoff:3.500A) Processing helix chain 'A' and resid 2273 through 2288 Processing helix chain 'A' and resid 2290 through 2298 removed outlier: 3.599A pdb=" N VAL A2296 " --> pdb=" O GLY A2292 " (cutoff:3.500A) Processing helix chain 'A' and resid 2302 through 2322 Processing helix chain 'A' and resid 2355 through 2371 removed outlier: 3.709A pdb=" N THR A2359 " --> pdb=" O PRO A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2384 removed outlier: 4.222A pdb=" N SER A2384 " --> pdb=" O LYS A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2403 Processing helix chain 'A' and resid 2404 through 2412 removed outlier: 4.626A pdb=" N SER A2409 " --> pdb=" O PRO A2405 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR A2410 " --> pdb=" O LEU A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2420 removed outlier: 3.616A pdb=" N TRP A2418 " --> pdb=" O PRO A2414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A2420 " --> pdb=" O LEU A2416 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2442 Processing helix chain 'A' and resid 2444 through 2459 Processing helix chain 'A' and resid 2462 through 2478 Processing helix chain 'A' and resid 2499 through 2515 removed outlier: 3.798A pdb=" N ALA A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2565 removed outlier: 3.632A pdb=" N LYS A2548 " --> pdb=" O ARG A2544 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A2551 " --> pdb=" O ARG A2547 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A2556 " --> pdb=" O ILE A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2599 Processing helix chain 'A' and resid 2620 through 2628 removed outlier: 3.554A pdb=" N ASN A2628 " --> pdb=" O VAL A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2669 through 2683 removed outlier: 3.759A pdb=" N CYS A2673 " --> pdb=" O ASP A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2710 removed outlier: 3.799A pdb=" N GLU A2701 " --> pdb=" O ILE A2697 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2733 removed outlier: 3.708A pdb=" N PHE A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2755 Proline residue: A2746 - end of helix Processing helix chain 'A' and resid 2764 through 2774 removed outlier: 4.405A pdb=" N LEU A2768 " --> pdb=" O PRO A2764 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A2774 " --> pdb=" O GLU A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2777 through 2793 removed outlier: 4.176A pdb=" N ARG A2781 " --> pdb=" O HIS A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2803 through 2819 removed outlier: 3.702A pdb=" N TYR A2811 " --> pdb=" O VAL A2807 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A2818 " --> pdb=" O SER A2814 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A2819 " --> pdb=" O ASN A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2827 through 2845 Processing helix chain 'A' and resid 2855 through 2866 removed outlier: 3.574A pdb=" N GLN A2859 " --> pdb=" O ALA A2855 " (cutoff:3.500A) Processing helix chain 'A' and resid 2873 through 2890 Processing helix chain 'A' and resid 2898 through 2903 Processing helix chain 'A' and resid 2913 through 2931 Processing helix chain 'A' and resid 2954 through 2970 Processing helix chain 'A' and resid 2971 through 2990 Proline residue: A2983 - end of helix removed outlier: 3.501A pdb=" N PHE A2990 " --> pdb=" O LEU A2986 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 2994 Processing helix chain 'A' and resid 2995 through 3004 removed outlier: 3.618A pdb=" N ILE A3000 " --> pdb=" O MET A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3026 removed outlier: 3.547A pdb=" N MET A3014 " --> pdb=" O TYR A3010 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A3016 " --> pdb=" O GLN A3012 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS A3026 " --> pdb=" O PHE A3022 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3040 Processing helix chain 'A' and resid 3050 through 3065 Processing helix chain 'A' and resid 3071 through 3073 No H-bonds generated for 'chain 'A' and resid 3071 through 3073' Processing helix chain 'A' and resid 3074 through 3080 Processing helix chain 'A' and resid 3086 through 3103 removed outlier: 3.613A pdb=" N HIS A3103 " --> pdb=" O ASP A3099 " (cutoff:3.500A) Processing helix chain 'A' and resid 3107 through 3119 removed outlier: 4.044A pdb=" N VAL A3117 " --> pdb=" O ALA A3113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A3118 " --> pdb=" O PHE A3114 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A3119 " --> pdb=" O GLN A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3120 through 3122 No H-bonds generated for 'chain 'A' and resid 3120 through 3122' Processing helix chain 'A' and resid 3128 through 3138 Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.559A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 157 through 173 Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 215 Processing helix chain 'B' and resid 260 through 281 removed outlier: 3.565A pdb=" N ASP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.728A pdb=" N LYS B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 365 1322 hydrogen bonds defined for protein. 3846 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: 8.70 Time building geometry restraints manager: 9.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3867 1.33 - 1.45: 4919 1.45 - 1.57: 12328 1.57 - 1.69: 0 1.69 - 1.82: 190 Bond restraints: 21304 Sorted by residual: bond pdb=" C LEU A2982 " pdb=" N PRO A2983 " ideal model delta sigma weight residual 1.335 1.389 -0.054 1.38e-02 5.25e+03 1.56e+01 bond pdb=" C GLN A1447 " pdb=" N LYS A1448 " ideal model delta sigma weight residual 1.335 1.383 -0.049 1.31e-02 5.83e+03 1.38e+01 bond pdb=" N GLN A2270 " pdb=" CA GLN A2270 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N CYS A1049 " pdb=" CA CYS A1049 " ideal model delta sigma weight residual 1.458 1.524 -0.066 1.90e-02 2.77e+03 1.21e+01 bond pdb=" N ILE A2995 " pdb=" CA ILE A2995 " ideal model delta sigma weight residual 1.460 1.490 -0.030 8.60e-03 1.35e+04 1.21e+01 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 477 105.81 - 112.95: 11955 112.95 - 120.09: 7892 120.09 - 127.23: 8356 127.23 - 134.37: 254 Bond angle restraints: 28934 Sorted by residual: angle pdb=" N THR A 310 " pdb=" CA THR A 310 " pdb=" C THR A 310 " ideal model delta sigma weight residual 113.88 103.10 10.78 1.23e+00 6.61e-01 7.68e+01 angle pdb=" CA PRO A1936 " pdb=" C PRO A1936 " pdb=" N PRO A1937 " ideal model delta sigma weight residual 117.93 125.23 -7.30 1.20e+00 6.94e-01 3.70e+01 angle pdb=" N VAL A1066 " pdb=" CA VAL A1066 " pdb=" C VAL A1066 " ideal model delta sigma weight residual 111.58 105.65 5.93 1.06e+00 8.90e-01 3.13e+01 angle pdb=" N LEU A 106 " pdb=" CA LEU A 106 " pdb=" C LEU A 106 " ideal model delta sigma weight residual 113.43 106.80 6.63 1.26e+00 6.30e-01 2.77e+01 angle pdb=" N LEU A 153 " pdb=" CA LEU A 153 " pdb=" C LEU A 153 " ideal model delta sigma weight residual 111.07 105.51 5.56 1.07e+00 8.73e-01 2.70e+01 ... (remaining 28929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11571 17.92 - 35.84: 1053 35.84 - 53.75: 250 53.75 - 71.67: 52 71.67 - 89.59: 33 Dihedral angle restraints: 12959 sinusoidal: 5141 harmonic: 7818 Sorted by residual: dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -28.45 -57.55 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" C ASP A1468 " pdb=" N ASP A1468 " pdb=" CA ASP A1468 " pdb=" CB ASP A1468 " ideal model delta harmonic sigma weight residual -122.60 -135.04 12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA GLN A1761 " pdb=" C GLN A1761 " pdb=" N LEU A1762 " pdb=" CA LEU A1762 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 12956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3067 0.073 - 0.147: 297 0.147 - 0.220: 71 0.220 - 0.293: 11 0.293 - 0.366: 4 Chirality restraints: 3450 Sorted by residual: chirality pdb=" CA LEU A 940 " pdb=" N LEU A 940 " pdb=" C LEU A 940 " pdb=" CB LEU A 940 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ASP A1468 " pdb=" N ASP A1468 " pdb=" C ASP A1468 " pdb=" CB ASP A1468 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A3121 " pdb=" CA VAL A3121 " pdb=" CG1 VAL A3121 " pdb=" CG2 VAL A3121 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 3447 not shown) Planarity restraints: 3650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2267 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE A2267 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A2267 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS A2268 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1064 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C CYS A1064 " 0.051 2.00e-02 2.50e+03 pdb=" O CYS A1064 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A1065 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A2521 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ALA A2521 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA A2521 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A2522 " -0.015 2.00e-02 2.50e+03 ... (remaining 3647 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 115 2.54 - 3.13: 16700 3.13 - 3.72: 34129 3.72 - 4.31: 48871 4.31 - 4.90: 78552 Nonbonded interactions: 178367 Sorted by model distance: nonbonded pdb=" O ASN A2628 " pdb=" OD1 ASN A2628 " model vdw 1.953 3.040 nonbonded pdb=" OH TYR A2614 " pdb=" OD2 ASP A2711 " model vdw 2.202 2.440 nonbonded pdb=" O LEU A1617 " pdb=" OG SER A1657 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR A2300 " pdb=" OD2 ASP A2429 " model vdw 2.226 2.440 nonbonded pdb=" O ASP A1628 " pdb=" OD1 ASP A1628 " model vdw 2.231 3.040 ... (remaining 178362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.020 Extract box with map and model: 18.350 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 58.680 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21304 Z= 0.384 Angle : 0.808 10.776 28934 Z= 0.521 Chirality : 0.053 0.366 3450 Planarity : 0.005 0.051 3650 Dihedral : 15.456 89.588 7839 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.29 % Favored : 93.41 % Rotamer: Outliers : 0.56 % Allowed : 11.72 % Favored : 87.72 % Cbeta Deviations : 0.04 % 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: -2.11 (0.15), residues: 2625 helix: -0.90 (0.11), residues: 1854 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 190 HIS 0.006 0.001 HIS A 685 PHE 0.032 0.002 PHE A2990 TYR 0.021 0.002 TYR A2576 ARG 0.004 0.000 ARG A1697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 424 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8345 (m-40) cc_final: 0.7875 (m110) REVERT: A 109 CYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4426 (t) REVERT: A 837 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7865 (mmp) REVERT: A 1887 LYS cc_start: 0.7119 (tmtt) cc_final: 0.6075 (mmtt) REVERT: A 2039 ASN cc_start: 0.8131 (m-40) cc_final: 0.6689 (m-40) REVERT: A 2749 CYS cc_start: 0.7695 (m) cc_final: 0.7384 (m) REVERT: B 344 MET cc_start: 0.8921 (mtp) cc_final: 0.8670 (mtm) outliers start: 13 outliers final: 4 residues processed: 433 average time/residue: 1.5212 time to fit residues: 739.1581 Evaluate side-chains 244 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 238 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 2545 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 68 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 241 optimal weight: 7.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 169 GLN A 246 ASN A 366 HIS A 906 GLN A1539 HIS A1596 GLN A1630 HIS A1637 ASN A1847 HIS A1892 ASN A2134 ASN A2139 ASN A2270 GLN A2305 HIS A2383 ASN A2628 ASN A2671 HIS B 106 GLN B 291 HIS B 323 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21304 Z= 0.210 Angle : 0.606 9.678 28934 Z= 0.307 Chirality : 0.039 0.164 3450 Planarity : 0.004 0.046 3650 Dihedral : 5.008 45.292 2865 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.93 % Rotamer: Outliers : 2.96 % Allowed : 16.49 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2625 helix: 0.70 (0.12), residues: 1861 sheet: None (None), residues: 0 loop : -1.68 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 190 HIS 0.007 0.001 HIS A2915 PHE 0.037 0.002 PHE A3045 TYR 0.018 0.001 TYR A2576 ARG 0.008 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 262 time to evaluate : 2.424 Fit side-chains REVERT: A 103 ASN cc_start: 0.8352 (m-40) cc_final: 0.8102 (m110) REVERT: A 278 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 380 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: A 394 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 876 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: A 1818 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 1887 LYS cc_start: 0.7236 (tmtt) cc_final: 0.6117 (mmtt) REVERT: A 2056 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7890 (ttt90) REVERT: A 2206 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mtmm) REVERT: A 2886 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8134 (ttt90) REVERT: A 2897 ASP cc_start: 0.7120 (p0) cc_final: 0.6696 (p0) REVERT: A 3086 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: A 3130 ARG cc_start: 0.6941 (tpt-90) cc_final: 0.6538 (tpt-90) REVERT: B 344 MET cc_start: 0.8905 (mtp) cc_final: 0.8634 (mtm) outliers start: 69 outliers final: 12 residues processed: 307 average time/residue: 1.3677 time to fit residues: 479.4540 Evaluate side-chains 250 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1818 ASP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2300 THR Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2778 LEU Chi-restraints excluded: chain A residue 2854 SER Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 3086 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 194 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 246 ASN A2054 HIS A2139 ASN A2189 HIS A2218 GLN A2443 GLN A2499 GLN A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2993 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21304 Z= 0.216 Angle : 0.574 10.070 28934 Z= 0.287 Chirality : 0.039 0.150 3450 Planarity : 0.004 0.050 3650 Dihedral : 4.492 27.272 2855 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.31 % Rotamer: Outliers : 3.01 % Allowed : 17.60 % Favored : 79.39 % 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: 0.78 (0.17), residues: 2625 helix: 1.28 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1853 HIS 0.006 0.001 HIS A2915 PHE 0.027 0.001 PHE A2990 TYR 0.015 0.001 TYR A2576 ARG 0.011 0.000 ARG A3035 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 255 time to evaluate : 2.226 Fit side-chains REVERT: A 148 VAL cc_start: 0.8684 (t) cc_final: 0.8395 (t) REVERT: A 278 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8515 (m) REVERT: A 286 THR cc_start: 0.8680 (t) cc_final: 0.8402 (m) REVERT: A 380 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: A 394 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 876 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: A 1887 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6037 (mmtt) REVERT: A 1890 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: A 2056 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7947 (ttt90) REVERT: A 2206 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8027 (mtmm) REVERT: A 2381 LYS cc_start: 0.8030 (tppt) cc_final: 0.7824 (tptt) REVERT: A 2547 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7454 (mtm110) REVERT: A 2886 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (ttt90) REVERT: A 2897 ASP cc_start: 0.7126 (p0) cc_final: 0.6715 (p0) REVERT: A 3030 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: A 3086 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: B 106 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5903 (pt0) REVERT: B 137 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6762 (mm-40) REVERT: B 344 MET cc_start: 0.8920 (mtp) cc_final: 0.8652 (mtm) outliers start: 70 outliers final: 13 residues processed: 299 average time/residue: 1.3388 time to fit residues: 455.7826 Evaluate side-chains 251 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1890 MET Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2706 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2904 LEU Chi-restraints excluded: chain A residue 3030 GLN Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 137 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 0.0980 chunk 257 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2993 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21304 Z= 0.196 Angle : 0.567 10.405 28934 Z= 0.281 Chirality : 0.039 0.209 3450 Planarity : 0.004 0.050 3650 Dihedral : 4.341 26.831 2853 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 2.45 % Allowed : 18.68 % Favored : 78.88 % 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: 1.11 (0.17), residues: 2625 helix: 1.54 (0.12), residues: 1867 sheet: None (None), residues: 0 loop : -1.30 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.006 0.001 HIS A2826 PHE 0.025 0.001 PHE A2990 TYR 0.013 0.001 TYR A2576 ARG 0.008 0.000 ARG A3035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 244 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 380 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: A 394 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8627 (tt) REVERT: A 876 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: A 890 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: A 1887 LYS cc_start: 0.7226 (tmtt) cc_final: 0.5508 (ptmt) REVERT: A 2056 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7918 (ttt90) REVERT: A 2206 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (mtmm) REVERT: A 2381 LYS cc_start: 0.7983 (tppt) cc_final: 0.7742 (tptt) REVERT: A 2547 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7433 (mtm110) REVERT: A 2886 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8083 (ttt90) REVERT: A 2897 ASP cc_start: 0.7137 (p0) cc_final: 0.6765 (p0) REVERT: A 3086 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: B 106 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.5940 (pt0) REVERT: B 210 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 344 MET cc_start: 0.8913 (mtp) cc_final: 0.8634 (mtm) outliers start: 57 outliers final: 14 residues processed: 280 average time/residue: 1.4223 time to fit residues: 452.4358 Evaluate side-chains 254 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2904 LEU Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 219 optimal weight: 0.0270 chunk 177 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A2139 ASN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS A2993 GLN B 164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21304 Z= 0.218 Angle : 0.576 12.240 28934 Z= 0.286 Chirality : 0.039 0.220 3450 Planarity : 0.004 0.054 3650 Dihedral : 4.310 30.736 2853 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 2.62 % Allowed : 19.02 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.25 (0.17), residues: 2625 helix: 1.63 (0.12), residues: 1875 sheet: None (None), residues: 0 loop : -1.25 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1853 HIS 0.005 0.001 HIS A2915 PHE 0.024 0.001 PHE A2990 TYR 0.014 0.001 TYR A2576 ARG 0.009 0.000 ARG A3035 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 247 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 380 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 394 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 876 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: A 890 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 1887 LYS cc_start: 0.7180 (tmtt) cc_final: 0.5473 (ptmt) REVERT: A 2206 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8014 (mtmm) REVERT: A 2536 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8093 (mptp) REVERT: A 2547 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7386 (mtm110) REVERT: A 2628 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7713 (p0) REVERT: A 2886 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8104 (ttt90) REVERT: A 2897 ASP cc_start: 0.7115 (p0) cc_final: 0.6694 (p0) REVERT: A 3086 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 92 GLU cc_start: 0.7239 (tp30) cc_final: 0.6959 (mm-30) REVERT: B 106 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.6014 (pt0) REVERT: B 137 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6681 (mm-40) REVERT: B 344 MET cc_start: 0.8922 (mtp) cc_final: 0.8645 (mtm) outliers start: 61 outliers final: 21 residues processed: 290 average time/residue: 1.3228 time to fit residues: 437.4894 Evaluate side-chains 254 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2246 GLU Chi-restraints excluded: chain A residue 2536 LYS Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2904 LEU Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.8980 chunk 231 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 213 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2055 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21304 Z= 0.204 Angle : 0.572 9.493 28934 Z= 0.284 Chirality : 0.038 0.184 3450 Planarity : 0.004 0.053 3650 Dihedral : 4.245 27.332 2853 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 2.75 % Allowed : 18.89 % Favored : 78.36 % 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: 1.42 (0.17), residues: 2625 helix: 1.75 (0.12), residues: 1874 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1853 HIS 0.005 0.001 HIS A2826 PHE 0.023 0.001 PHE A2990 TYR 0.013 0.001 TYR A2576 ARG 0.010 0.000 ARG A2683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 380 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 394 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8676 (tt) REVERT: A 876 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: A 890 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: A 1887 LYS cc_start: 0.7124 (tmtt) cc_final: 0.5907 (mmpt) REVERT: A 2056 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7951 (ttt90) REVERT: A 2206 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7989 (mtmm) REVERT: A 2536 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8123 (mptp) REVERT: A 2628 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 2886 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8217 (ttt90) REVERT: A 3086 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: B 92 GLU cc_start: 0.7251 (tp30) cc_final: 0.6939 (mm-30) REVERT: B 106 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5905 (pt0) REVERT: B 210 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (tp) REVERT: B 297 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8371 (tttt) REVERT: B 344 MET cc_start: 0.8916 (mtp) cc_final: 0.8639 (mtm) outliers start: 64 outliers final: 25 residues processed: 284 average time/residue: 1.3791 time to fit residues: 449.2475 Evaluate side-chains 262 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2536 LYS Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2717 ASN Chi-restraints excluded: chain A residue 2739 ILE Chi-restraints excluded: chain A residue 2740 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 3032 SER Chi-restraints excluded: chain A residue 3044 ASN Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 0.0870 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 256 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1459 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21304 Z= 0.199 Angle : 0.571 9.128 28934 Z= 0.282 Chirality : 0.038 0.154 3450 Planarity : 0.004 0.058 3650 Dihedral : 4.187 24.495 2853 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 2.66 % Allowed : 19.54 % Favored : 77.80 % 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: 1.56 (0.17), residues: 2625 helix: 1.84 (0.12), residues: 1873 sheet: None (None), residues: 0 loop : -1.05 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.005 0.001 HIS A2915 PHE 0.023 0.001 PHE A2990 TYR 0.016 0.001 TYR A2845 ARG 0.014 0.000 ARG A3035 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8499 (m) REVERT: A 380 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: A 394 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 749 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: A 876 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: A 890 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 1233 TYR cc_start: 0.7031 (m-10) cc_final: 0.6084 (m-10) REVERT: A 1309 MET cc_start: 0.8704 (mmm) cc_final: 0.8491 (mmt) REVERT: A 1887 LYS cc_start: 0.7153 (tmtt) cc_final: 0.5888 (mmpt) REVERT: A 2056 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (ttt90) REVERT: A 2206 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7971 (mtmm) REVERT: A 2536 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8110 (mptp) REVERT: A 2628 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7655 (p0) REVERT: A 2886 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8237 (ttt90) REVERT: A 3086 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: B 92 GLU cc_start: 0.7223 (tp30) cc_final: 0.6947 (mm-30) REVERT: B 106 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5860 (pt0) REVERT: B 210 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8304 (tp) REVERT: B 297 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8339 (tttt) REVERT: B 344 MET cc_start: 0.8915 (mtp) cc_final: 0.8638 (mtm) outliers start: 62 outliers final: 22 residues processed: 279 average time/residue: 1.4287 time to fit residues: 453.0294 Evaluate side-chains 255 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2065 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2536 LYS Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2854 SER Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 153 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 0.4980 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21304 Z= 0.197 Angle : 0.586 11.948 28934 Z= 0.285 Chirality : 0.038 0.204 3450 Planarity : 0.004 0.059 3650 Dihedral : 4.143 22.170 2853 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 2.28 % Allowed : 20.61 % Favored : 77.11 % 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: 1.67 (0.17), residues: 2625 helix: 1.91 (0.12), residues: 1875 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.005 0.001 HIS A2915 PHE 0.020 0.001 PHE A2990 TYR 0.012 0.001 TYR A2576 ARG 0.013 0.000 ARG A2683 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 749 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: A 876 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: A 890 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: A 1309 MET cc_start: 0.8699 (mmm) cc_final: 0.8394 (mmt) REVERT: A 1887 LYS cc_start: 0.7146 (tmtt) cc_final: 0.5405 (ptmt) REVERT: A 2206 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7976 (mtmm) REVERT: A 2536 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (mptp) REVERT: A 2628 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 2886 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: A 3086 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: B 92 GLU cc_start: 0.7164 (tp30) cc_final: 0.6906 (mm-30) REVERT: B 106 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5876 (pt0) REVERT: B 210 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8308 (tp) REVERT: B 297 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8339 (tttt) REVERT: B 344 MET cc_start: 0.8912 (mtp) cc_final: 0.8634 (mtm) outliers start: 53 outliers final: 24 residues processed: 269 average time/residue: 1.3558 time to fit residues: 415.4698 Evaluate side-chains 252 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2162 GLN Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2536 LYS Chi-restraints excluded: chain A residue 2545 PHE Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 2993 GLN Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21304 Z= 0.233 Angle : 0.594 12.092 28934 Z= 0.292 Chirality : 0.039 0.189 3450 Planarity : 0.004 0.061 3650 Dihedral : 4.168 21.752 2853 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.50 % Rotamer: Outliers : 2.19 % Allowed : 20.57 % Favored : 77.24 % 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: 1.62 (0.17), residues: 2625 helix: 1.88 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.021 0.001 HIS A2830 PHE 0.017 0.001 PHE A2211 TYR 0.013 0.001 TYR B 298 ARG 0.014 0.000 ARG A3035 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8697 (tt) REVERT: A 749 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: A 876 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: A 890 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 1233 TYR cc_start: 0.7088 (m-10) cc_final: 0.6223 (m-10) REVERT: A 1887 LYS cc_start: 0.7142 (tmtt) cc_final: 0.5392 (ptmt) REVERT: A 2206 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: A 2536 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8175 (mptp) REVERT: A 2628 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7655 (p0) REVERT: A 2886 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8220 (ttt90) REVERT: A 3086 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: B 92 GLU cc_start: 0.7186 (tp30) cc_final: 0.6924 (mm-30) REVERT: B 106 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: B 137 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.6680 (mm-40) REVERT: B 344 MET cc_start: 0.8925 (mtp) cc_final: 0.8643 (mtm) outliers start: 51 outliers final: 26 residues processed: 259 average time/residue: 1.3706 time to fit residues: 405.7837 Evaluate side-chains 256 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1960 GLN Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2065 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2206 LYS Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2536 LYS Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain A residue 3086 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 211 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 0.0470 chunk 167 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A1637 ASN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21304 Z= 0.185 Angle : 0.585 12.222 28934 Z= 0.284 Chirality : 0.038 0.172 3450 Planarity : 0.004 0.062 3650 Dihedral : 4.102 21.505 2853 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 1.72 % Allowed : 21.12 % Favored : 77.16 % 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: 1.77 (0.17), residues: 2625 helix: 1.99 (0.12), residues: 1871 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.016 0.001 HIS A2830 PHE 0.016 0.001 PHE A2990 TYR 0.012 0.001 TYR A2576 ARG 0.014 0.000 ARG A2683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 749 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: A 876 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 890 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 1233 TYR cc_start: 0.7046 (m-10) cc_final: 0.6211 (m-10) REVERT: A 1887 LYS cc_start: 0.7074 (tmtt) cc_final: 0.5344 (ptmt) REVERT: A 2628 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 92 GLU cc_start: 0.7110 (tp30) cc_final: 0.6868 (mm-30) REVERT: B 106 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6255 (pt0) REVERT: B 297 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8361 (tttt) REVERT: B 344 MET cc_start: 0.8904 (mtp) cc_final: 0.8632 (mtm) outliers start: 40 outliers final: 23 residues processed: 252 average time/residue: 1.3596 time to fit residues: 391.4815 Evaluate side-chains 250 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain A residue 1465 CYS Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1960 GLN Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2065 ARG Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2239 SER Chi-restraints excluded: chain A residue 2628 ASN Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2771 SER Chi-restraints excluded: chain A residue 2837 THR Chi-restraints excluded: chain A residue 2854 SER Chi-restraints excluded: chain A residue 2875 ILE Chi-restraints excluded: chain A residue 2907 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 264 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A1637 ASN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101706 restraints weight = 26975.972| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.02 r_work: 0.3046 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21304 Z= 0.221 Angle : 0.599 11.942 28934 Z= 0.291 Chirality : 0.038 0.170 3450 Planarity : 0.004 0.060 3650 Dihedral : 4.116 20.810 2853 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 1.67 % Allowed : 21.43 % Favored : 76.90 % 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: 1.77 (0.17), residues: 2625 helix: 1.98 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1853 HIS 0.014 0.001 HIS A2830 PHE 0.017 0.001 PHE A2211 TYR 0.013 0.001 TYR A2576 ARG 0.015 0.000 ARG A2683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8075.88 seconds wall clock time: 144 minutes 54.23 seconds (8694.23 seconds total)