Starting phenix.real_space_refine on Sat Aug 3 00:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/08_2024/8tze_41756.cif" } resolution = 2.9 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 4018 2.51 5 N 1061 2.21 5 O 1133 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1745": "OE1" <-> "OE2" Residue "A GLU 1790": "OE1" <-> "OE2" Residue "A PHE 1792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1828": "OD1" <-> "OD2" Residue "A ASP 1873": "OD1" <-> "OD2" Residue "A GLU 1878": "OE1" <-> "OE2" Residue "A GLU 1882": "OE1" <-> "OE2" Residue "A PHE 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1902": "OE1" <-> "OE2" Residue "A TYR 1992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1994": "OD1" <-> "OD2" Residue "A TYR 2057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2098": "OE1" <-> "OE2" Residue "A ASP 2175": "OD1" <-> "OD2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2212": "OE1" <-> "OE2" Residue "A GLU 2230": "OE1" <-> "OE2" Residue "A GLU 2239": "OE1" <-> "OE2" Residue "A PHE 2324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A ASP 2377": "OD1" <-> "OD2" Residue "A TYR 2475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2512": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6255 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6216 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 35, 'TRANS': 751} Chain breaks: 13 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.74, per 1000 atoms: 0.92 Number of scatterers: 6255 At special positions: 0 Unit cell: (90.695, 136.51, 86.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 3 9.00 O 1133 8.00 N 1061 7.00 C 4018 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 31.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 1629 through 1631 No H-bonds generated for 'chain 'A' and resid 1629 through 1631' Processing helix chain 'A' and resid 1650 through 1656 Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1703 through 1713 Processing helix chain 'A' and resid 1770 through 1791 Processing helix chain 'A' and resid 1827 through 1837 Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 3.645A pdb=" N ILE A1860 " --> pdb=" O PRO A1857 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1861 " --> pdb=" O ASP A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1873 No H-bonds generated for 'chain 'A' and resid 1871 through 1873' Processing helix chain 'A' and resid 1880 through 1889 removed outlier: 6.407A pdb=" N LEU A1885 " --> pdb=" O GLU A1882 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY A1886 " --> pdb=" O PHE A1883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A1887 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A1888 " --> pdb=" O LEU A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1926 removed outlier: 4.245A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.660A pdb=" N GLN A1960 " --> pdb=" O ASP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1966 Processing helix chain 'A' and resid 1967 through 1988 removed outlier: 3.571A pdb=" N ALA A1988 " --> pdb=" O TYR A1984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2046 Processing helix chain 'A' and resid 2051 through 2068 Processing helix chain 'A' and resid 2070 through 2074 removed outlier: 4.357A pdb=" N ILE A2073 " --> pdb=" O GLY A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2100 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.534A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.619A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2282 Processing helix chain 'A' and resid 2339 through 2344 Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2395 removed outlier: 3.554A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2522 Processing sheet with id=AA1, first strand: chain 'A' and resid 1626 through 1627 Processing sheet with id=AA2, first strand: chain 'A' and resid 1732 through 1733 removed outlier: 6.225A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1839 through 1841 Processing sheet with id=AA4, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 6.543A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AA6, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.844A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 3.899A pdb=" N GLN A2178 " --> pdb=" O CYS A2171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2199 through 2205 Processing sheet with id=AA9, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 3.976A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2300 through 2305 removed outlier: 6.387A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 3.524A pdb=" N THR A2356 " --> pdb=" O ALA A2366 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A2373 " --> pdb=" O LEU A2386 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A2386 " --> pdb=" O VAL A2373 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A2375 " --> pdb=" O CYS A2384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2414 through 2420 removed outlier: 5.994A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 732 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: 2.44 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1029 1.31 - 1.43: 1573 1.43 - 1.56: 3711 1.56 - 1.68: 2 1.68 - 1.81: 60 Bond restraints: 6375 Sorted by residual: bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.456 1.302 0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.466 1.312 0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.467 1.317 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.451 1.303 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C20 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.456 1.323 0.133 2.00e-02 2.50e+03 4.43e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 96.32 - 112.96: 3682 112.96 - 129.59: 4903 129.59 - 146.22: 49 146.22 - 162.86: 0 162.86 - 179.49: 2 Bond angle restraints: 8636 Sorted by residual: angle pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " ideal model delta sigma weight residual 120.77 113.37 7.40 9.70e-01 1.06e+00 5.82e+01 angle pdb=" N TRP A1734 " pdb=" CA TRP A1734 " pdb=" C TRP A1734 " ideal model delta sigma weight residual 108.34 98.62 9.72 1.31e+00 5.83e-01 5.51e+01 angle pdb=" O ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " ideal model delta sigma weight residual 120.48 126.96 -6.48 8.90e-01 1.26e+00 5.30e+01 angle pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta sigma weight residual 119.84 111.83 8.01 1.25e+00 6.40e-01 4.11e+01 angle pdb=" N PRO A1942 " pdb=" CA PRO A1942 " pdb=" C PRO A1942 " ideal model delta sigma weight residual 112.47 99.99 12.48 2.06e+00 2.36e-01 3.67e+01 ... (remaining 8631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3514 17.91 - 35.81: 234 35.81 - 53.72: 80 53.72 - 71.63: 14 71.63 - 89.53: 7 Dihedral angle restraints: 3849 sinusoidal: 1570 harmonic: 2279 Sorted by residual: dihedral pdb=" CD ARG A2522 " pdb=" NE ARG A2522 " pdb=" CZ ARG A2522 " pdb=" NH1 ARG A2522 " ideal model delta sinusoidal sigma weight residual 0.00 -56.21 56.21 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLY A2100 " pdb=" C GLY A2100 " pdb=" N CYS A2101 " pdb=" CA CYS A2101 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 639 0.035 - 0.071: 249 0.071 - 0.106: 68 0.106 - 0.142: 41 0.142 - 0.177: 5 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA PRO A1942 " pdb=" N PRO A1942 " pdb=" C PRO A1942 " pdb=" CB PRO A1942 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA GLN A1960 " pdb=" N GLN A1960 " pdb=" C GLN A1960 " pdb=" CB GLN A1960 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE A2323 " pdb=" N ILE A2323 " pdb=" C ILE A2323 " pdb=" CB ILE A2323 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 999 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2522 " 0.892 9.50e-02 1.11e+02 4.00e-01 9.71e+01 pdb=" NE ARG A2522 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A2522 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A2522 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2522 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " 0.092 5.00e-02 4.00e+02 1.49e-01 3.57e+01 pdb=" N PRO A1942 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2456 " 0.408 9.50e-02 1.11e+02 1.83e-01 2.06e+01 pdb=" NE ARG A2456 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A2456 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A2456 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2456 " 0.016 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 146 2.69 - 3.24: 5665 3.24 - 3.80: 9344 3.80 - 4.35: 13196 4.35 - 4.90: 21995 Nonbonded interactions: 50346 Sorted by model distance: nonbonded pdb=" O ASP A2269 " pdb=" OD1 ASP A2269 " model vdw 2.140 3.040 nonbonded pdb=" OE1 GLN A1845 " pdb=" NE ARG A1847 " model vdw 2.195 3.120 nonbonded pdb=" O GLU A1797 " pdb=" OG1 THR A1806 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A2213 " pdb=" OG1 THR A2229 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A1954 " pdb=" OD1 ASP A1956 " model vdw 2.210 3.040 ... (remaining 50341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.007 0.154 6375 Z= 0.437 Angle : 0.764 12.484 8636 Z= 0.438 Chirality : 0.045 0.177 1002 Planarity : 0.015 0.400 1080 Dihedral : 14.565 89.533 2367 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 13.91 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 759 helix: 1.34 (0.40), residues: 191 sheet: 0.33 (0.35), residues: 206 loop : -0.68 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1734 HIS 0.005 0.001 HIS A2391 PHE 0.028 0.002 PHE A2326 TYR 0.014 0.001 TYR A1984 ARG 0.005 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2379 LYS cc_start: 0.7850 (mttt) cc_final: 0.7486 (mtmm) REVERT: A 2467 LYS cc_start: 0.6750 (tptt) cc_final: 0.6425 (tppt) REVERT: A 2509 LYS cc_start: 0.7555 (mttt) cc_final: 0.7012 (tttm) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 1.1876 time to fit residues: 118.8062 Evaluate side-chains 85 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 2219 THR Chi-restraints excluded: chain A residue 2290 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6375 Z= 0.192 Angle : 0.550 5.752 8636 Z= 0.291 Chirality : 0.045 0.150 1002 Planarity : 0.005 0.076 1080 Dihedral : 6.154 53.946 870 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 2.75 % Allowed : 13.77 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.24 (0.31), residues: 759 helix: 1.27 (0.39), residues: 204 sheet: 0.33 (0.35), residues: 206 loop : -0.56 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1811 HIS 0.005 0.001 HIS A2510 PHE 0.020 0.001 PHE A2326 TYR 0.013 0.002 TYR A2346 ARG 0.009 0.001 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7673 (t0) cc_final: 0.5931 (p0) REVERT: A 2379 LYS cc_start: 0.7809 (mttt) cc_final: 0.7436 (mtmm) REVERT: A 2456 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7963 (ttm110) REVERT: A 2467 LYS cc_start: 0.6518 (tptt) cc_final: 0.6185 (tppt) REVERT: A 2509 LYS cc_start: 0.7628 (mttt) cc_final: 0.6949 (pptt) outliers start: 19 outliers final: 8 residues processed: 88 average time/residue: 1.2428 time to fit residues: 115.2579 Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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: 0.7282 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6375 Z= 0.189 Angle : 0.541 5.667 8636 Z= 0.285 Chirality : 0.044 0.149 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.799 53.758 866 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.74 % Allowed : 14.78 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.22 (0.31), residues: 759 helix: 1.29 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1734 HIS 0.004 0.000 HIS A2510 PHE 0.015 0.001 PHE A2326 TYR 0.010 0.001 TYR A1699 ARG 0.007 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7672 (t0) cc_final: 0.5930 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7435 (mtmm) REVERT: A 2467 LYS cc_start: 0.6516 (tptt) cc_final: 0.6184 (tppt) REVERT: A 2509 LYS cc_start: 0.7628 (mttt) cc_final: 0.6949 (pptt) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 1.2774 time to fit residues: 104.9190 Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6375 Z= 0.189 Angle : 0.541 5.667 8636 Z= 0.285 Chirality : 0.044 0.149 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.800 53.758 866 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.30 % Allowed : 15.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.22 (0.31), residues: 759 helix: 1.29 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1734 HIS 0.004 0.000 HIS A2510 PHE 0.015 0.001 PHE A2326 TYR 0.010 0.001 TYR A1699 ARG 0.007 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7672 (t0) cc_final: 0.5930 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7435 (mtmm) REVERT: A 2467 LYS cc_start: 0.6516 (tptt) cc_final: 0.6184 (tppt) REVERT: A 2509 LYS cc_start: 0.7627 (mttt) cc_final: 0.6949 (pptt) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 1.1970 time to fit residues: 95.8043 Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6375 Z= 0.189 Angle : 0.541 5.668 8636 Z= 0.285 Chirality : 0.044 0.149 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.819 53.760 866 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.30 % Allowed : 15.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.22 (0.31), residues: 759 helix: 1.29 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1734 HIS 0.004 0.000 HIS A2510 PHE 0.015 0.001 PHE A2326 TYR 0.009 0.001 TYR A1699 ARG 0.007 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7672 (t0) cc_final: 0.5930 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7435 (mtmm) REVERT: A 2467 LYS cc_start: 0.6516 (tptt) cc_final: 0.6184 (tppt) REVERT: A 2509 LYS cc_start: 0.7628 (mttt) cc_final: 0.6949 (pptt) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 1.2126 time to fit residues: 97.2369 Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 0.0030 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6375 Z= 0.189 Angle : 0.540 5.667 8636 Z= 0.285 Chirality : 0.044 0.149 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.870 53.780 866 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.30 % Allowed : 15.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.22 (0.31), residues: 759 helix: 1.29 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1734 HIS 0.004 0.000 HIS A2510 PHE 0.014 0.001 PHE A2326 TYR 0.009 0.001 TYR A2449 ARG 0.007 0.000 ARG A1847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7672 (t0) cc_final: 0.5930 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7435 (mtmm) REVERT: A 2467 LYS cc_start: 0.6516 (tptt) cc_final: 0.6184 (tppt) REVERT: A 2509 LYS cc_start: 0.7628 (mttt) cc_final: 0.6948 (pptt) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 1.2361 time to fit residues: 98.9786 Evaluate side-chains 82 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 chunk 75 optimal weight: 0.0030 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 overall best weight: 0.2666 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6375 Z= 0.158 Angle : 0.538 5.694 8636 Z= 0.285 Chirality : 0.044 0.151 1002 Planarity : 0.005 0.064 1080 Dihedral : 5.758 53.629 866 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.59 % Allowed : 15.51 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.24 (0.31), residues: 759 helix: 1.32 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.011 0.001 PHE A2275 TYR 0.010 0.001 TYR A2475 ARG 0.009 0.001 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7670 (t0) cc_final: 0.5933 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7434 (mtmm) REVERT: A 2467 LYS cc_start: 0.6494 (tptt) cc_final: 0.6178 (tppt) REVERT: A 2509 LYS cc_start: 0.7625 (mttt) cc_final: 0.6947 (pptt) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 1.2295 time to fit residues: 104.8977 Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0170 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6375 Z= 0.158 Angle : 0.538 5.694 8636 Z= 0.285 Chirality : 0.044 0.151 1002 Planarity : 0.005 0.064 1080 Dihedral : 5.758 53.629 866 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.24 (0.31), residues: 759 helix: 1.32 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.011 0.001 PHE A2275 TYR 0.010 0.001 TYR A2475 ARG 0.009 0.001 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7670 (t0) cc_final: 0.5933 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7434 (mtmm) REVERT: A 2467 LYS cc_start: 0.6494 (tptt) cc_final: 0.6178 (tppt) REVERT: A 2509 LYS cc_start: 0.7625 (mttt) cc_final: 0.6947 (pptt) outliers start: 9 outliers final: 9 residues processed: 78 average time/residue: 1.2207 time to fit residues: 100.4846 Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6375 Z= 0.158 Angle : 0.538 5.694 8636 Z= 0.285 Chirality : 0.044 0.151 1002 Planarity : 0.005 0.064 1080 Dihedral : 5.758 53.629 866 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.24 (0.31), residues: 759 helix: 1.32 (0.39), residues: 204 sheet: 0.31 (0.35), residues: 206 loop : -0.58 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.011 0.001 PHE A2275 TYR 0.010 0.001 TYR A2475 ARG 0.009 0.001 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7670 (t0) cc_final: 0.5933 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7434 (mtmm) REVERT: A 2467 LYS cc_start: 0.6494 (tptt) cc_final: 0.6178 (tppt) REVERT: A 2509 LYS cc_start: 0.7625 (mttt) cc_final: 0.6947 (pptt) outliers start: 9 outliers final: 9 residues processed: 78 average time/residue: 1.1953 time to fit residues: 98.3072 Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6375 Z= 0.380 Angle : 0.576 5.650 8636 Z= 0.303 Chirality : 0.048 0.151 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.768 54.111 866 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.20 (0.31), residues: 759 helix: 1.24 (0.39), residues: 204 sheet: 0.34 (0.35), residues: 206 loop : -0.60 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1811 HIS 0.005 0.001 HIS A2510 PHE 0.021 0.002 PHE A2326 TYR 0.012 0.002 TYR A1747 ARG 0.004 0.001 ARG A2443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 1994 ASP cc_start: 0.7718 (t0) cc_final: 0.5935 (p0) REVERT: A 2379 LYS cc_start: 0.7810 (mttt) cc_final: 0.7433 (mtmm) REVERT: A 2467 LYS cc_start: 0.6509 (tptt) cc_final: 0.6190 (tppt) REVERT: A 2509 LYS cc_start: 0.7642 (mttt) cc_final: 0.6959 (pptt) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 1.2278 time to fit residues: 98.2219 Evaluate side-chains 80 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 TRP Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.181810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142556 restraints weight = 7103.535| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.51 r_work: 0.3522 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6375 Z= 0.380 Angle : 0.576 5.650 8636 Z= 0.303 Chirality : 0.048 0.151 1002 Planarity : 0.005 0.065 1080 Dihedral : 5.769 54.111 866 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.20 (0.31), residues: 759 helix: 1.24 (0.39), residues: 204 sheet: 0.34 (0.35), residues: 206 loop : -0.60 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1811 HIS 0.005 0.001 HIS A2510 PHE 0.021 0.002 PHE A2326 TYR 0.012 0.002 TYR A1747 ARG 0.004 0.001 ARG A2443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.16 seconds wall clock time: 45 minutes 53.28 seconds (2753.28 seconds total)