Starting phenix.real_space_refine on Fri Dec 27 11:46:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.map" model { file = "/net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edo_28038/12_2024/8edo_28038.cif" } resolution = 3.4 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 11 5.16 5 C 2828 2.51 5 N 832 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4465 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1984 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 18, 'ASN:plan1': 16, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 2481 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 14, 'TRANS': 402} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 998 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 123 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 12, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 269 Time building chain proxies: 3.32, per 1000 atoms: 0.74 Number of scatterers: 4465 At special positions: 0 Unit cell: (109.2, 102.96, 83.2, 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 11 16.00 O 794 8.00 N 832 7.00 C 2828 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 - 3.00 Amino acid : True - 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: 1.26 Conformation dependent library (CDL) restraints added in 707.3 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 1041 through 1049 removed outlier: 3.693A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1136 through 1156 removed outlier: 4.345A pdb=" N SER A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1165 removed outlier: 3.590A pdb=" N SER A1164 " --> pdb=" O GLY A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1172 through 1188 Processing helix chain 'A' and resid 1828 through 1842 removed outlier: 3.706A pdb=" N THR A1832 " --> pdb=" O ASP A1828 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1864 Processing helix chain 'A' and resid 1883 through 1898 Processing helix chain 'A' and resid 1903 through 1914 removed outlier: 4.081A pdb=" N SER A1914 " --> pdb=" O ILE A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1931 through 1937 Processing helix chain 'A' and resid 1943 through 1964 Processing helix chain 'A' and resid 1967 through 1980 removed outlier: 4.123A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A1978 " --> pdb=" O LYS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2001 Processing helix chain 'A' and resid 2004 through 2019 removed outlier: 3.993A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 removed outlier: 3.693A pdb=" N LEU B1167 " --> pdb=" O SER B1164 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B1168 " --> pdb=" O ILE B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1828 through 1842 removed outlier: 4.058A pdb=" N ILE B1836 " --> pdb=" O THR B1832 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY B1842 " --> pdb=" O LEU B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1883 through 1898 Processing helix chain 'B' and resid 1903 through 1916 removed outlier: 3.863A pdb=" N SER B1914 " --> pdb=" O ILE B1910 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS B1915 " --> pdb=" O SER B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1933 Proline residue: B1930 - end of helix removed outlier: 4.085A pdb=" N SER B1933 " --> pdb=" O THR B1929 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1937 Processing helix chain 'B' and resid 1943 through 1964 Processing helix chain 'B' and resid 1967 through 1980 removed outlier: 3.828A pdb=" N GLY B1977 " --> pdb=" O ALA B1973 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B1978 " --> pdb=" O LYS B1974 " (cutoff:3.500A) 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 2001 Processing helix chain 'B' and resid 2004 through 2021 removed outlier: 3.793A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2040 Processing helix chain 'B' and resid 2041 through 2043 No H-bonds generated for 'chain 'B' and resid 2041 through 2043' Processing helix chain 'B' and resid 2047 through 2052 removed outlier: 6.684A pdb=" N LEU B2052 " --> pdb=" O GLU B2049 " (cutoff:3.500A) Processing helix chain 'B' and resid 2053 through 2069 removed outlier: 3.596A pdb=" N ARG B2062 " --> pdb=" O ALA B2058 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B2063 " --> pdb=" O ILE B2059 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2070 through 2072 No H-bonds generated for 'chain 'B' and resid 2070 through 2072' Processing helix chain 'B' and resid 2074 through 2090 Proline residue: B2080 - end of helix Processing helix chain 'B' and resid 2094 through 2114 Processing helix chain 'B' and resid 2121 through 2135 Processing helix chain 'B' and resid 2137 through 2144 removed outlier: 3.653A pdb=" N TYR B2141 " --> pdb=" O LEU B2137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B2142 " --> pdb=" O PRO B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.610A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2197 Processing helix chain 'B' and resid 2203 through 2217 removed outlier: 3.952A pdb=" N PHE B2215 " --> pdb=" O LEU B2211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B2217 " --> pdb=" O GLN B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2222 through 2235 removed outlier: 4.246A pdb=" N ARG B2226 " --> pdb=" O SER B2222 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B2229 " --> pdb=" O PRO B2225 " (cutoff:3.500A) Processing helix chain 'B' and resid 2239 through 2260 Processing helix chain 'B' and resid 2262 through 2281 removed outlier: 3.720A pdb=" N SER B2266 " --> pdb=" O ASP B2262 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1176 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: 1.28 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1564 1.34 - 1.45: 483 1.45 - 1.57: 2455 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 4523 Sorted by residual: bond pdb=" N GLU A1868 " pdb=" CA GLU A1868 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.53e+00 bond pdb=" CG LEU A1848 " pdb=" CD1 LEU A1848 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" CA GLU A1868 " pdb=" CB GLU A1868 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.23e+00 bond pdb=" CG LEU A1841 " pdb=" CD2 LEU A1841 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB PHE B2088 " pdb=" CG PHE B2088 " ideal model delta sigma weight residual 1.502 1.480 0.022 2.30e-02 1.89e+03 8.99e-01 ... (remaining 4518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 6090 1.75 - 3.50: 100 3.50 - 5.25: 19 5.25 - 7.00: 3 7.00 - 8.75: 5 Bond angle restraints: 6217 Sorted by residual: angle pdb=" N LYS A1171 " pdb=" CA LYS A1171 " pdb=" C LYS A1171 " ideal model delta sigma weight residual 114.75 108.04 6.71 1.26e+00 6.30e-01 2.83e+01 angle pdb=" C ILE A1867 " pdb=" N GLU A1868 " pdb=" CA GLU A1868 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C GLU A1926 " pdb=" N TYR A1927 " pdb=" CA TYR A1927 " ideal model delta sigma weight residual 122.38 115.97 6.41 1.81e+00 3.05e-01 1.25e+01 angle pdb=" CA LYS A1171 " pdb=" C LYS A1171 " pdb=" N ASP A1172 " ideal model delta sigma weight residual 119.80 115.42 4.38 1.34e+00 5.57e-01 1.07e+01 angle pdb=" N GLU A1868 " pdb=" CA GLU A1868 " pdb=" CB GLU A1868 " ideal model delta sigma weight residual 110.49 115.57 -5.08 1.69e+00 3.50e-01 9.04e+00 ... (remaining 6212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.14: 2394 12.14 - 24.29: 116 24.29 - 36.43: 58 36.43 - 48.58: 15 48.58 - 60.72: 5 Dihedral angle restraints: 2588 sinusoidal: 401 harmonic: 2187 Sorted by residual: dihedral pdb=" CA MET B1967 " pdb=" C MET B1967 " pdb=" N TYR B1968 " pdb=" CA TYR B1968 " ideal model delta harmonic sigma weight residual 180.00 -165.02 -14.98 0 5.00e+00 4.00e-02 8.97e+00 dihedral pdb=" CA GLY A1160 " pdb=" C GLY A1160 " pdb=" N LEU A1161 " pdb=" CA LEU A1161 " ideal model delta harmonic sigma weight residual -180.00 -165.21 -14.79 0 5.00e+00 4.00e-02 8.75e+00 dihedral pdb=" CA GLN A1972 " pdb=" CB GLN A1972 " pdb=" CG GLN A1972 " pdb=" CD GLN A1972 " ideal model delta sinusoidal sigma weight residual -60.00 -106.20 46.20 3 1.50e+01 4.44e-03 8.30e+00 ... (remaining 2585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 435 0.032 - 0.064: 261 0.064 - 0.096: 63 0.096 - 0.128: 18 0.128 - 0.160: 3 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA GLU A1868 " pdb=" N GLU A1868 " pdb=" C GLU A1868 " pdb=" CB GLU A1868 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB THR A1108 " pdb=" CA THR A1108 " pdb=" OG1 THR A1108 " pdb=" CG2 THR A1108 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CG LEU A1856 " pdb=" CB LEU A1856 " pdb=" CD1 LEU A1856 " pdb=" CD2 LEU A1856 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 777 not shown) Planarity restraints: 827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1103 " -0.010 2.00e-02 2.50e+03 1.48e-02 3.85e+00 pdb=" CG PHE A1103 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A1103 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1103 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A1103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1103 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1905 " -0.011 2.00e-02 2.50e+03 8.64e-03 1.31e+00 pdb=" CG PHE A1905 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A1905 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A1905 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1905 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1905 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1905 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2248 " -0.080 9.50e-02 1.11e+02 3.61e-02 1.06e+00 pdb=" NE ARG B2248 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B2248 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B2248 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B2248 " 0.000 2.00e-02 2.50e+03 ... (remaining 824 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1332 2.81 - 3.33: 4486 3.33 - 3.86: 7009 3.86 - 4.38: 6841 4.38 - 4.90: 12607 Nonbonded interactions: 32275 Sorted by model distance: nonbonded pdb=" O PHE B1913 " pdb=" NZ LYS B1921 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG A1849 " pdb=" O ILE A1879 " model vdw 2.391 3.120 nonbonded pdb=" O ALA B2216 " pdb=" NE2 GLN B2224 " model vdw 2.414 3.120 nonbonded pdb=" O ILE B1918 " pdb=" ND1 HIS B1922 " model vdw 2.424 3.120 nonbonded pdb=" O MET A1180 " pdb=" OG1 THR A1184 " model vdw 2.440 3.040 ... (remaining 32270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.004 0.041 4523 Z= 0.283 Angle : 0.612 8.747 6217 Z= 0.342 Chirality : 0.042 0.160 780 Planarity : 0.003 0.036 827 Dihedral : 11.347 60.719 1158 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.32), residues: 737 helix: 2.16 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -1.03 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1931 HIS 0.005 0.002 HIS B2051 PHE 0.034 0.002 PHE A1103 TYR 0.013 0.002 TYR A1927 ARG 0.009 0.001 ARG B2248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1728 time to fit residues: 13.2016 Evaluate side-chains 54 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4523 Z= 0.136 Angle : 0.461 6.993 6217 Z= 0.251 Chirality : 0.038 0.124 780 Planarity : 0.002 0.013 827 Dihedral : 3.429 15.508 766 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % 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: 2.66 (0.33), residues: 737 helix: 2.52 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -0.55 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1931 HIS 0.004 0.001 HIS B2084 PHE 0.012 0.001 PHE A1103 TYR 0.026 0.002 TYR A1927 ARG 0.002 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.507 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.1945 time to fit residues: 15.3300 Evaluate side-chains 57 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4523 Z= 0.234 Angle : 0.508 6.403 6217 Z= 0.275 Chirality : 0.040 0.120 780 Planarity : 0.002 0.025 827 Dihedral : 3.684 14.622 766 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.61 % 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: 2.28 (0.32), residues: 737 helix: 2.25 (0.23), residues: 546 sheet: None (None), residues: 0 loop : -0.72 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2054 HIS 0.003 0.001 HIS B2051 PHE 0.015 0.002 PHE A1103 TYR 0.018 0.002 TYR A1927 ARG 0.005 0.001 ARG B2248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.542 Fit side-chains REVERT: A 1041 MET cc_start: 0.4627 (pmm) cc_final: 0.4078 (ttp) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.1669 time to fit residues: 12.3103 Evaluate side-chains 56 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4523 Z= 0.193 Angle : 0.468 5.669 6217 Z= 0.257 Chirality : 0.039 0.121 780 Planarity : 0.002 0.020 827 Dihedral : 3.558 15.077 766 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 4.02 % Allowed : 18.39 % Favored : 77.59 % 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: 2.41 (0.32), residues: 737 helix: 2.26 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.51 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1976 HIS 0.003 0.001 HIS B2084 PHE 0.016 0.002 PHE A1103 TYR 0.019 0.002 TYR A1927 ARG 0.002 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.566 Fit side-chains REVERT: A 1041 MET cc_start: 0.4222 (pmm) cc_final: 0.3826 (ttp) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.1682 time to fit residues: 13.2771 Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2073 LEU Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4523 Z= 0.267 Angle : 0.528 5.861 6217 Z= 0.285 Chirality : 0.040 0.126 780 Planarity : 0.003 0.028 827 Dihedral : 3.825 15.467 766 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.61 % Favored : 95.25 % Rotamer: Outliers : 2.87 % Allowed : 21.84 % Favored : 75.29 % 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: 2.16 (0.32), residues: 737 helix: 2.15 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.70 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2054 HIS 0.004 0.001 HIS B2051 PHE 0.018 0.002 PHE A1103 TYR 0.018 0.002 TYR A1927 ARG 0.003 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.537 Fit side-chains REVERT: A 1041 MET cc_start: 0.4376 (pmm) cc_final: 0.4008 (ttp) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.1497 time to fit residues: 11.8269 Evaluate side-chains 61 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2073 LEU Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0770 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4523 Z= 0.134 Angle : 0.446 7.165 6217 Z= 0.241 Chirality : 0.037 0.130 780 Planarity : 0.002 0.012 827 Dihedral : 3.353 16.515 766 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.93 % Favored : 95.93 % Rotamer: Outliers : 4.02 % Allowed : 22.41 % Favored : 73.56 % 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: 2.79 (0.33), residues: 737 helix: 2.56 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1976 HIS 0.004 0.001 HIS B2084 PHE 0.014 0.001 PHE B1905 TYR 0.018 0.001 TYR A1927 ARG 0.001 0.000 ARG B2226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.546 Fit side-chains REVERT: A 1041 MET cc_start: 0.4041 (pmm) cc_final: 0.3776 (ttp) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.1705 time to fit residues: 13.6073 Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 0.0060 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4523 Z= 0.136 Angle : 0.470 7.651 6217 Z= 0.249 Chirality : 0.038 0.168 780 Planarity : 0.002 0.013 827 Dihedral : 3.245 15.661 766 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.30 % Allowed : 22.99 % Favored : 74.71 % 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: 3.01 (0.33), residues: 737 helix: 2.70 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.20 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1976 HIS 0.003 0.001 HIS B2084 PHE 0.023 0.001 PHE A1103 TYR 0.018 0.001 TYR A1927 ARG 0.002 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.679 Fit side-chains REVERT: A 1041 MET cc_start: 0.4020 (pmm) cc_final: 0.3792 (ttp) REVERT: A 1113 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7970 (tt) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1730 time to fit residues: 13.3662 Evaluate side-chains 58 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4523 Z= 0.157 Angle : 0.508 12.438 6217 Z= 0.262 Chirality : 0.039 0.211 780 Planarity : 0.002 0.014 827 Dihedral : 3.268 13.055 766 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % 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: 3.00 (0.33), residues: 737 helix: 2.68 (0.23), residues: 549 sheet: None (None), residues: 0 loop : -0.17 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1976 HIS 0.003 0.001 HIS B2084 PHE 0.028 0.001 PHE A1103 TYR 0.017 0.002 TYR A1927 ARG 0.002 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.545 Fit side-chains REVERT: A 1106 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5187 (t80) REVERT: A 1113 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7845 (tt) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.1649 time to fit residues: 12.3123 Evaluate side-chains 59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 ASN Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4523 Z= 0.171 Angle : 0.521 12.069 6217 Z= 0.269 Chirality : 0.039 0.162 780 Planarity : 0.002 0.031 827 Dihedral : 3.361 18.050 766 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.45 % Allowed : 21.84 % Favored : 74.71 % 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: 2.92 (0.33), residues: 737 helix: 2.62 (0.23), residues: 549 sheet: None (None), residues: 0 loop : -0.17 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1976 HIS 0.003 0.001 HIS B2084 PHE 0.022 0.001 PHE B1905 TYR 0.017 0.002 TYR A1927 ARG 0.009 0.001 ARG B2248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.481 Fit side-chains REVERT: A 1106 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5172 (t80) REVERT: A 1113 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7850 (tt) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.1529 time to fit residues: 11.4265 Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 ASN Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4523 Z= 0.154 Angle : 0.506 11.110 6217 Z= 0.262 Chirality : 0.039 0.190 780 Planarity : 0.002 0.015 827 Dihedral : 3.251 15.602 766 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.02 % Allowed : 20.11 % Favored : 75.86 % 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: 3.03 (0.33), residues: 737 helix: 2.69 (0.23), residues: 549 sheet: None (None), residues: 0 loop : -0.09 (0.51), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1976 HIS 0.003 0.001 HIS B2084 PHE 0.029 0.001 PHE A1103 TYR 0.017 0.001 TYR A1927 ARG 0.002 0.000 ARG A1176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.514 Fit side-chains REVERT: A 1106 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5135 (t80) REVERT: A 1180 MET cc_start: 0.8187 (mtm) cc_final: 0.7756 (mtm) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.1569 time to fit residues: 11.8648 Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1106 TYR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1156 ASN Chi-restraints excluded: chain A residue 1844 SER Chi-restraints excluded: chain B residue 2205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.124873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105738 restraints weight = 11438.802| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.03 r_work: 0.3575 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4523 Z= 0.127 Angle : 0.491 9.596 6217 Z= 0.251 Chirality : 0.038 0.175 780 Planarity : 0.002 0.012 827 Dihedral : 3.077 15.868 766 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.87 % Allowed : 22.99 % Favored : 74.14 % 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: 3.29 (0.33), residues: 737 helix: 2.86 (0.23), residues: 548 sheet: None (None), residues: 0 loop : 0.05 (0.51), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1976 HIS 0.003 0.001 HIS A1163 PHE 0.027 0.001 PHE A1103 TYR 0.017 0.001 TYR A1927 ARG 0.002 0.000 ARG B2248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.41 seconds wall clock time: 21 minutes 7.67 seconds (1267.67 seconds total)