Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 13:10:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/10_2023/6x9o_22106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/10_2023/6x9o_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_22106/10_2023/6x9o_22106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/10_2023/6x9o_22106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/10_2023/6x9o_22106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/10_2023/6x9o_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 10.98, 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: 7.97 Conformation dependent library (CDL) restraints added in 3.0 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: 2.30 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: 8.13 Time building geometry restraints manager: 8.61 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.600 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.710 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.800 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 433 average time/residue: 1.5365 time to fit residues: 747.9232 Evaluate side-chains 240 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.2103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 169 GLN A 366 HIS A 898 HIS A 906 GLN A1539 HIS A1596 GLN A1630 HIS A1637 ASN A1847 HIS A1892 ASN A2054 HIS A2134 ASN A2139 ASN A2189 HIS A2305 HIS A2383 ASN A2628 ASN A2671 HIS B 106 GLN B 164 HIS B 291 HIS B 323 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21304 Z= 0.242 Angle : 0.622 9.577 28934 Z= 0.314 Chirality : 0.040 0.172 3450 Planarity : 0.004 0.046 3650 Dihedral : 4.743 23.422 2853 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.03 % Favored : 94.82 % Rotamer: Outliers : 3.18 % Allowed : 16.23 % Favored : 80.59 % 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: -0.03 (0.16), residues: 2625 helix: 0.68 (0.12), residues: 1861 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 764 *********************** 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 336 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 262 time to evaluate : 2.381 Fit side-chains outliers start: 74 outliers final: 16 residues processed: 311 average time/residue: 1.3760 time to fit residues: 488.8684 Evaluate side-chains 248 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.367 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.4085 time to fit residues: 6.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 201 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 261 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A1524 GLN A2139 ASN A2218 GLN A2443 GLN A2499 GLN A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21304 Z= 0.258 Angle : 0.594 9.572 28934 Z= 0.299 Chirality : 0.040 0.153 3450 Planarity : 0.004 0.052 3650 Dihedral : 4.570 22.307 2853 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 2.88 % Allowed : 17.48 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2625 helix: 1.16 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -1.41 (0.23), residues: 749 *********************** 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 320 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 253 time to evaluate : 2.537 Fit side-chains outliers start: 67 outliers final: 24 residues processed: 297 average time/residue: 1.3238 time to fit residues: 450.6083 Evaluate side-chains 255 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 0.5448 time to fit residues: 9.9832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 242 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 69 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 169 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.037 21304 Z= 0.233 Angle : 0.582 8.279 28934 Z= 0.290 Chirality : 0.039 0.157 3450 Planarity : 0.004 0.052 3650 Dihedral : 4.435 22.093 2853 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Rotamer: Outliers : 2.83 % Allowed : 18.25 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2625 helix: 1.45 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 753 *********************** 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 312 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 246 time to evaluate : 2.421 Fit side-chains outliers start: 66 outliers final: 20 residues processed: 286 average time/residue: 1.4085 time to fit residues: 465.2731 Evaluate side-chains 249 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.2872 time to fit residues: 5.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.8980 chunk 145 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2183 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21304 Z= 0.219 Angle : 0.579 8.943 28934 Z= 0.287 Chirality : 0.039 0.165 3450 Planarity : 0.004 0.053 3650 Dihedral : 4.351 21.930 2853 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 2.19 % Allowed : 19.41 % Favored : 78.40 % 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: 1.20 (0.17), residues: 2625 helix: 1.60 (0.12), residues: 1874 sheet: None (None), residues: 0 loop : -1.26 (0.23), residues: 751 *********************** 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 291 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 2.615 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 275 average time/residue: 1.3341 time to fit residues: 421.6700 Evaluate side-chains 245 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 6 average time/residue: 0.4529 time to fit residues: 7.0815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.7980 chunk 231 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21304 Z= 0.210 Angle : 0.573 8.201 28934 Z= 0.284 Chirality : 0.038 0.153 3450 Planarity : 0.004 0.054 3650 Dihedral : 4.269 21.776 2853 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.31 % Rotamer: Outliers : 3.01 % Allowed : 18.98 % Favored : 78.02 % 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: 1.35 (0.17), residues: 2625 helix: 1.70 (0.12), residues: 1877 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 748 *********************** 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 307 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 237 time to evaluate : 2.245 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 285 average time/residue: 1.2628 time to fit residues: 412.0912 Evaluate side-chains 251 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 8 average time/residue: 0.4026 time to fit residues: 6.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: