Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 01:05:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moc_23924/10_2023/7moc_23924.pdb" } resolution = 4.56 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= 0.007 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 98 5.16 5 C 8943 2.51 5 N 2321 2.21 5 O 2521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A GLU 924": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1873": "OE1" <-> "OE2" Residue "A GLU 1898": "OE1" <-> "OE2" Residue "A GLU 1904": "OE1" <-> "OE2" Residue "A GLU 1907": "OE1" <-> "OE2" Residue "A GLU 1908": "OE1" <-> "OE2" Residue "A GLU 1964": "OE1" <-> "OE2" Residue "A GLU 2008": "OE1" <-> "OE2" Residue "B GLU 1898": "OE1" <-> "OE2" Residue "B GLU 1907": "OE1" <-> "OE2" Residue "B GLU 1908": "OE1" <-> "OE2" Residue "B GLU 1919": "OE1" <-> "OE2" Residue "B GLU 1926": "OE1" <-> "OE2" Residue "B GLU 1964": "OE1" <-> "OE2" Residue "B GLU 2008": "OE1" <-> "OE2" Residue "B GLU 2049": "OE1" <-> "OE2" Residue "B GLU 2122": "OE1" <-> "OE2" Residue "B GLU 2123": "OE1" <-> "OE2" Residue "B GLU 2134": "OE1" <-> "OE2" Residue "B GLU 2172": "OE1" <-> "OE2" Residue "B GLU 2174": "OE1" <-> "OE2" Residue "B GLU 2182": "OE1" <-> "OE2" Residue "B GLU 2186": "OE1" <-> "OE2" Residue "B GLU 2190": "OE1" <-> "OE2" Residue "B GLU 2193": "OE1" <-> "OE2" Residue "B GLU 2210": "OE1" <-> "OE2" Residue "B GLU 2255": "OE1" <-> "OE2" Residue "B GLU 2271": "OE1" <-> "OE2" Residue "B PHE 2295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2306": "OE1" <-> "OE2" Residue "B GLU 2318": "OE1" <-> "OE2" Residue "B GLU 2336": "OE1" <-> "OE2" Residue "B GLU 2347": "OE1" <-> "OE2" Residue "B GLU 2409": "OE1" <-> "OE2" Residue "B GLU 2426": "OE1" <-> "OE2" Residue "B GLU 2427": "OE1" <-> "OE2" Residue "B GLU 2612": "OE1" <-> "OE2" Residue "B GLU 2620": "OE1" <-> "OE2" Residue "B GLU 2624": "OE1" <-> "OE2" Residue "B GLU 2708": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 13883 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8562 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 32, 'TRANS': 1049} Chain breaks: 28 Chain: "B" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5321 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 27, 'TRANS': 645} Chain breaks: 6 Time building chain proxies: 7.60, per 1000 atoms: 0.55 Number of scatterers: 13883 At special positions: 0 Unit cell: (146.862, 157.608, 113.43, 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 98 16.00 O 2521 8.00 N 2321 7.00 C 8943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.697A pdb=" N TRP A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.952A pdb=" N GLU A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 166 removed outlier: 4.227A pdb=" N ASN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 removed outlier: 3.600A pdb=" N GLU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 4.440A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.689A pdb=" N TYR A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 259 through 276 Proline residue: A 268 - end of helix removed outlier: 3.587A pdb=" N ILE A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.757A pdb=" N TYR A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 358 removed outlier: 4.879A pdb=" N VAL A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.618A pdb=" N ALA A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 434 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 484 through 503 Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.843A pdb=" N ASN A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.855A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 586 Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'A' and resid 679 through 696 removed outlier: 4.140A pdb=" N TRP A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 723 removed outlier: 3.766A pdb=" N ARG A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 753 through 766 removed outlier: 3.722A pdb=" N ARG A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 849 through 852 Processing helix chain 'A' and resid 890 through 903 removed outlier: 4.191A pdb=" N VAL A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 925 removed outlier: 3.590A pdb=" N LEU A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 943 Processing helix chain 'A' and resid 956 through 974 Processing helix chain 'A' and resid 978 through 984 removed outlier: 3.681A pdb=" N HIS A 982 " --> pdb=" O GLY A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1002 removed outlier: 3.858A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 Processing helix chain 'A' and resid 1026 through 1028 No H-bonds generated for 'chain 'A' and resid 1026 through 1028' Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 3.519A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1080 Processing helix chain 'A' and resid 1093 through 1118 Processing helix chain 'A' and resid 1134 through 1156 Processing helix chain 'A' and resid 1156 through 1170 removed outlier: 5.918A pdb=" N MET A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A1166 " --> pdb=" O MET A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1190 Processing helix chain 'A' and resid 1830 through 1842 removed outlier: 3.558A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1863 Processing helix chain 'A' and resid 1883 through 1898 Processing helix chain 'A' and resid 1900 through 1916 removed outlier: 4.689A pdb=" N GLU A1904 " --> pdb=" O HIS A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1941 Proline residue: A1930 - end of helix removed outlier: 4.412A pdb=" N SER A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1934 " --> pdb=" O PRO A1930 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A1935 " --> pdb=" O TRP A1931 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A1936 " --> pdb=" O LEU A1932 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG A1937 " --> pdb=" O SER A1933 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A1938 " --> pdb=" O ASN A1934 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A1939 " --> pdb=" O LEU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1964 Processing helix chain 'A' and resid 1967 through 1981 removed outlier: 3.699A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1998 Processing helix chain 'A' and resid 2006 through 2020 removed outlier: 3.522A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A2019 " --> pdb=" O VAL A2015 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A2020 " --> pdb=" O ALA A2016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1843 Processing helix chain 'B' and resid 1883 through 1898 Processing helix chain 'B' and resid 1900 through 1916 removed outlier: 4.206A pdb=" N GLU B1904 " --> pdb=" O HIS B1900 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B1915 " --> pdb=" O SER B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1929 Processing helix chain 'B' and resid 1930 through 1933 removed outlier: 3.625A pdb=" N SER B1933 " --> pdb=" O PRO B1930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1930 through 1933' Processing helix chain 'B' and resid 1934 through 1940 removed outlier: 4.028A pdb=" N PHE B1938 " --> pdb=" O ASN B1934 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS B1939 " --> pdb=" O LEU B1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1964 removed outlier: 3.730A pdb=" N ARG B1947 " --> pdb=" O ASP B1943 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1981 Processing helix chain 'B' and resid 1982 through 1984 No H-bonds generated for 'chain 'B' and resid 1982 through 1984' Processing helix chain 'B' and resid 1985 through 1999 Processing helix chain 'B' and resid 2004 through 2021 removed outlier: 3.784A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2043 removed outlier: 3.764A pdb=" N CYS B2041 " --> pdb=" O ILE B2037 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B2043 " --> pdb=" O LYS B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2047 through 2051 Processing helix chain 'B' and resid 2053 through 2090 removed outlier: 3.849A pdb=" N PHE B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B2070 " --> pdb=" O MET B2066 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B2073 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B2076 " --> pdb=" O SER B2072 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B2077 " --> pdb=" O LEU B2073 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS B2078 " --> pdb=" O ASP B2074 " (cutoff:3.500A) Proline residue: B2080 - end of helix Processing helix chain 'B' and resid 2094 through 2114 Processing helix chain 'B' and resid 2121 through 2136 Processing helix chain 'B' and resid 2137 through 2144 Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.816A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2199 removed outlier: 3.720A pdb=" N LEU B2181 " --> pdb=" O ALA B2177 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B2198 " --> pdb=" O ALA B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2218 Processing helix chain 'B' and resid 2223 through 2235 Processing helix chain 'B' and resid 2239 through 2259 Processing helix chain 'B' and resid 2265 through 2281 Processing helix chain 'B' and resid 2282 through 2284 No H-bonds generated for 'chain 'B' and resid 2282 through 2284' Processing helix chain 'B' and resid 2289 through 2304 removed outlier: 3.533A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2328 through 2333 removed outlier: 4.136A pdb=" N ASP B2332 " --> pdb=" O ILE B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2334 through 2358 removed outlier: 3.641A pdb=" N ILE B2342 " --> pdb=" O VAL B2338 " (cutoff:3.500A) Proline residue: B2345 - end of helix removed outlier: 4.655A pdb=" N TRP B2348 " --> pdb=" O ASN B2344 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N HIS B2349 " --> pdb=" O PRO B2345 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B2352 " --> pdb=" O TRP B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2379 removed outlier: 3.693A pdb=" N LYS B2375 " --> pdb=" O GLY B2371 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B2376 " --> pdb=" O HIS B2372 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B2377 " --> pdb=" O LEU B2373 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B2378 " --> pdb=" O LEU B2374 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B2379 " --> pdb=" O LYS B2375 " (cutoff:3.500A) Processing helix chain 'B' and resid 2381 through 2404 removed outlier: 3.944A pdb=" N ARG B2403 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2414 through 2422 Processing helix chain 'B' and resid 2425 through 2430 Processing helix chain 'B' and resid 2592 through 2609 Processing helix chain 'B' and resid 2611 through 2629 Processing helix chain 'B' and resid 2633 through 2651 removed outlier: 3.578A pdb=" N HIS B2637 " --> pdb=" O PHE B2633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN B2638 " --> pdb=" O PRO B2634 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU B2639 " --> pdb=" O VAL B2635 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B2642 " --> pdb=" O ASN B2638 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2670 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2679 through 2686 removed outlier: 4.337A pdb=" N GLN B2683 " --> pdb=" O THR B2679 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B2685 " --> pdb=" O TYR B2681 " (cutoff:3.500A) Processing helix chain 'B' and resid 2688 through 2694 removed outlier: 4.328A pdb=" N ARG B2692 " --> pdb=" O ASN B2688 " (cutoff:3.500A) Processing helix chain 'B' and resid 2704 through 2722 1042 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3492 1.33 - 1.45: 2703 1.45 - 1.58: 7776 1.58 - 1.70: 1 1.70 - 1.82: 148 Bond restraints: 14120 Sorted by residual: bond pdb=" C LEU A1187 " pdb=" N GLN A1188 " ideal model delta sigma weight residual 1.333 1.443 -0.110 1.49e-02 4.50e+03 5.46e+01 bond pdb=" CA MET A 108 " pdb=" C MET A 108 " ideal model delta sigma weight residual 1.522 1.585 -0.063 1.39e-02 5.18e+03 2.06e+01 bond pdb=" CB THR A1832 " pdb=" OG1 THR A1832 " ideal model delta sigma weight residual 1.433 1.375 0.058 1.60e-02 3.91e+03 1.33e+01 bond pdb=" CA PHE B2069 " pdb=" C PHE B2069 " ideal model delta sigma weight residual 1.524 1.568 -0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA GLN A1188 " pdb=" C GLN A1188 " ideal model delta sigma weight residual 1.522 1.567 -0.045 1.37e-02 5.33e+03 1.08e+01 ... (remaining 14115 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.65: 96 102.65 - 110.71: 4264 110.71 - 118.77: 6980 118.77 - 126.82: 7592 126.82 - 134.88: 162 Bond angle restraints: 19094 Sorted by residual: angle pdb=" N ASP B2074 " pdb=" CA ASP B2074 " pdb=" C ASP B2074 " ideal model delta sigma weight residual 111.36 122.45 -11.09 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N THR A1893 " pdb=" CA THR A1893 " pdb=" C THR A1893 " ideal model delta sigma weight residual 111.14 101.97 9.17 1.08e+00 8.57e-01 7.21e+01 angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 111.07 102.16 8.91 1.07e+00 8.73e-01 6.94e+01 angle pdb=" N PHE B2693 " pdb=" CA PHE B2693 " pdb=" C PHE B2693 " ideal model delta sigma weight residual 111.28 119.93 -8.65 1.09e+00 8.42e-01 6.30e+01 angle pdb=" N SER A1891 " pdb=" CA SER A1891 " pdb=" C SER A1891 " ideal model delta sigma weight residual 111.11 120.47 -9.36 1.20e+00 6.94e-01 6.08e+01 ... (remaining 19089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 7945 18.39 - 36.78: 508 36.78 - 55.16: 72 55.16 - 73.55: 26 73.55 - 91.94: 11 Dihedral angle restraints: 8562 sinusoidal: 3413 harmonic: 5149 Sorted by residual: dihedral pdb=" C ASN A 734 " pdb=" N ASN A 734 " pdb=" CA ASN A 734 " pdb=" CB ASN A 734 " ideal model delta harmonic sigma weight residual -122.60 -142.60 20.00 0 2.50e+00 1.60e-01 6.40e+01 dihedral pdb=" C HIS B2078 " pdb=" N HIS B2078 " pdb=" CA HIS B2078 " pdb=" CB HIS B2078 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" C ASN B2071 " pdb=" N ASN B2071 " pdb=" CA ASN B2071 " pdb=" CB ASN B2071 " ideal model delta harmonic sigma weight residual -122.60 -138.92 16.32 0 2.50e+00 1.60e-01 4.26e+01 ... (remaining 8559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2085 0.158 - 0.316: 184 0.316 - 0.474: 18 0.474 - 0.631: 6 0.631 - 0.789: 5 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA ASN A 734 " pdb=" N ASN A 734 " pdb=" C ASN A 734 " pdb=" CB ASN A 734 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA HIS B2078 " pdb=" N HIS B2078 " pdb=" C HIS B2078 " pdb=" CB HIS B2078 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CB VAL B2606 " pdb=" CA VAL B2606 " pdb=" CG1 VAL B2606 " pdb=" CG2 VAL B2606 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 2295 not shown) Planarity restraints: 2351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1853 " -0.244 2.00e-02 2.50e+03 1.35e-01 3.66e+02 pdb=" CG TYR A1853 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1853 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 TYR A1853 " 0.107 2.00e-02 2.50e+03 pdb=" CE1 TYR A1853 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR A1853 " 0.076 2.00e-02 2.50e+03 pdb=" CZ TYR A1853 " 0.035 2.00e-02 2.50e+03 pdb=" OH TYR A1853 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B2693 " -0.137 2.00e-02 2.50e+03 8.35e-02 1.22e+02 pdb=" CG PHE B2693 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE B2693 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE B2693 " 0.081 2.00e-02 2.50e+03 pdb=" CE1 PHE B2693 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B2693 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE B2693 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 49 " -0.146 2.00e-02 2.50e+03 7.51e-02 1.13e+02 pdb=" CG TYR A 49 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 49 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR A 49 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 49 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 49 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 49 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 49 " -0.094 2.00e-02 2.50e+03 ... (remaining 2348 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 683 2.75 - 3.29: 15455 3.29 - 3.82: 23828 3.82 - 4.36: 29247 4.36 - 4.90: 48291 Nonbonded interactions: 117504 Sorted by model distance: nonbonded pdb=" CD1 LEU B1839 " pdb=" CD1 LEU B1920 " model vdw 2.211 3.880 nonbonded pdb=" OG SER B1916 " pdb=" CD2 LEU B1920 " model vdw 2.375 3.460 nonbonded pdb=" O LEU B2065 " pdb=" OG SER B2068 " model vdw 2.512 2.440 nonbonded pdb=" OD1 ASP A1845 " pdb=" OG SER A1847 " model vdw 2.515 2.440 nonbonded pdb=" OD1 ASN A 974 " pdb=" OG1 THR A 976 " model vdw 2.530 2.440 ... (remaining 117499 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 4.470 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 40.590 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.012 0.110 14120 Z= 0.770 Angle : 1.821 11.105 19094 Z= 1.229 Chirality : 0.106 0.789 2298 Planarity : 0.016 0.135 2351 Dihedral : 13.173 91.938 5172 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % Cbeta Deviations : 1.00 % 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: -0.04 (0.18), residues: 1683 helix: 0.25 (0.12), residues: 1344 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 711 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 713 average time/residue: 0.2628 time to fit residues: 273.2126 Evaluate side-chains 441 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS A 510 ASN A 608 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN A1835 ASN ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2319 GLN B2393 HIS B2615 GLN B2670 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14120 Z= 0.221 Angle : 0.644 7.936 19094 Z= 0.342 Chirality : 0.040 0.197 2298 Planarity : 0.004 0.041 2351 Dihedral : 5.018 29.475 1819 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.45 % Allowed : 2.48 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.20), residues: 1683 helix: 1.78 (0.13), residues: 1398 sheet: None (None), residues: 0 loop : 0.35 (0.41), residues: 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 530 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 531 average time/residue: 0.2302 time to fit residues: 183.8940 Evaluate side-chains 386 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN A1039 ASN A1115 ASN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2071 ASN B2638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14120 Z= 0.208 Angle : 0.622 9.492 19094 Z= 0.324 Chirality : 0.039 0.185 2298 Planarity : 0.004 0.044 2351 Dihedral : 4.780 26.759 1819 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.19 % Allowed : 2.16 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.20), residues: 1683 helix: 1.83 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : 0.33 (0.40), residues: 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 471 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 471 average time/residue: 0.2422 time to fit residues: 172.1787 Evaluate side-chains 369 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 712 HIS A 781 HIS A1039 ASN A1115 ASN A1170 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14120 Z= 0.224 Angle : 0.614 7.769 19094 Z= 0.321 Chirality : 0.038 0.215 2298 Planarity : 0.004 0.046 2351 Dihedral : 4.678 24.289 1819 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.13 % Allowed : 1.85 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 1683 helix: 1.79 (0.13), residues: 1399 sheet: None (None), residues: 0 loop : 0.40 (0.40), residues: 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 440 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 441 average time/residue: 0.2445 time to fit residues: 165.4232 Evaluate side-chains 360 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1579 time to fit residues: 2.6286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS A1039 ASN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14120 Z= 0.211 Angle : 0.612 11.716 19094 Z= 0.317 Chirality : 0.038 0.194 2298 Planarity : 0.004 0.058 2351 Dihedral : 4.641 23.884 1819 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.13 % Allowed : 1.53 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1683 helix: 1.83 (0.13), residues: 1395 sheet: None (None), residues: 0 loop : 0.41 (0.39), residues: 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 436 average time/residue: 0.2306 time to fit residues: 153.7740 Evaluate side-chains 360 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 712 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 HIS B1835 ASN ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2119 HIS ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14120 Z= 0.235 Angle : 0.626 9.964 19094 Z= 0.325 Chirality : 0.038 0.225 2298 Planarity : 0.004 0.046 2351 Dihedral : 4.617 23.419 1819 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1683 helix: 1.70 (0.13), residues: 1391 sheet: None (None), residues: 0 loop : 0.36 (0.39), residues: 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 420 average time/residue: 0.2196 time to fit residues: 142.4926 Evaluate side-chains 358 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1658 time to fit residues: 2.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 501 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN A1039 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2117 GLN B2413 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14120 Z= 0.267 Angle : 0.674 9.043 19094 Z= 0.351 Chirality : 0.040 0.229 2298 Planarity : 0.004 0.046 2351 Dihedral : 4.755 25.789 1819 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1683 helix: 1.53 (0.13), residues: 1389 sheet: None (None), residues: 0 loop : 0.43 (0.40), residues: 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.2292 time to fit residues: 147.0225 Evaluate side-chains 343 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 222 ASN A 412 ASN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2117 GLN ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2413 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14120 Z= 0.220 Angle : 0.679 8.620 19094 Z= 0.353 Chirality : 0.040 0.209 2298 Planarity : 0.004 0.050 2351 Dihedral : 4.688 23.483 1819 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.06 % Allowed : 0.83 % Favored : 99.11 % 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: 2.00 (0.20), residues: 1683 helix: 1.59 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : 0.32 (0.40), residues: 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.2281 time to fit residues: 148.8008 Evaluate side-chains 345 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN B1882 ASN ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2117 GLN B2119 HIS ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14120 Z= 0.222 Angle : 0.682 8.969 19094 Z= 0.353 Chirality : 0.041 0.286 2298 Planarity : 0.004 0.056 2351 Dihedral : 4.672 22.542 1819 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1683 helix: 1.61 (0.14), residues: 1383 sheet: None (None), residues: 0 loop : 0.23 (0.39), residues: 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.2155 time to fit residues: 137.0266 Evaluate side-chains 349 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 174 optimal weight: 0.0770 chunk 160 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1835 ASN ** A1840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1966 GLN ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2117 GLN ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14120 Z= 0.210 Angle : 0.698 8.773 19094 Z= 0.363 Chirality : 0.041 0.284 2298 Planarity : 0.004 0.058 2351 Dihedral : 4.702 24.308 1819 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % 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: 1.91 (0.21), residues: 1683 helix: 1.55 (0.14), residues: 1389 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 417 average time/residue: 0.2241 time to fit residues: 145.0022 Evaluate side-chains 353 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2117 GLN B2119 HIS B2303 GLN ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099216 restraints weight = 34249.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102781 restraints weight = 22507.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105427 restraints weight = 16037.525| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14120 Z= 0.254 Angle : 0.723 9.057 19094 Z= 0.378 Chirality : 0.042 0.288 2298 Planarity : 0.004 0.055 2351 Dihedral : 4.826 21.728 1819 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 1.71 (0.21), residues: 1683 helix: 1.44 (0.14), residues: 1395 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3341.37 seconds wall clock time: 61 minutes 28.78 seconds (3688.78 seconds total)