Starting phenix.real_space_refine on Mon Jan 13 21:38:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.map" model { file = "/net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jst_61782/01_2025/9jst_61782.cif" } resolution = 1.79 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= 0.010 sd= 0.099 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 8 5.16 5 C 1440 2.51 5 N 368 2.21 5 O 360 1.98 5 H 2128 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "E" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "G" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Time building chain proxies: 2.69, per 1000 atoms: 0.63 Number of scatterers: 4304 At special positions: 0 Unit cell: (73.7856, 75.5424, 49.1904, 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 8 16.00 O 360 8.00 N 368 7.00 C 1440 6.00 H 2128 1.00 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: 1.07 Conformation dependent library (CDL) restraints added in 330.9 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 77.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179 removed outlier: 6.866A pdb=" N LEU B 170 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER A 171 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 172 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 173 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 174 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 175 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 170 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER B 171 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 172 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY B 173 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 175 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 176 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 167 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU D 170 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY C 169 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N ILE D 172 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N SER C 171 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N THR D 174 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY C 173 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ARG D 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 175 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET D 178 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA C 177 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 164 removed outlier: 6.421A pdb=" N VAL G 150 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TRP H 153 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL G 152 " --> pdb=" O TRP H 153 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR H 155 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS G 154 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY H 157 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TRP G 156 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR H 159 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 158 " --> pdb=" O TYR H 159 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLN H 161 " --> pdb=" O GLN G 158 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP G 160 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU H 163 " --> pdb=" O TRP G 160 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 162 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179 removed outlier: 6.402A pdb=" N VAL E 167 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU F 170 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY E 169 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ILE F 172 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N SER E 171 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR F 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY E 173 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ARG F 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY E 175 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET F 178 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA E 177 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL F 167 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU G 170 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY F 169 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N ILE G 172 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N SER F 171 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N THR G 174 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY F 173 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ARG G 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY F 175 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N MET G 178 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA F 177 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU H 170 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER G 171 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE H 172 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY G 173 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 174 " --> pdb=" O GLY G 173 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 282 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: 1.29 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 2128 1.12 - 1.29: 296 1.29 - 1.47: 967 1.47 - 1.64: 977 1.64 - 1.81: 16 Bond restraints: 4384 Sorted by residual: bond pdb=" CD1 TRP C 153 " pdb=" HD1 TRP C 153 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 TRP B 156 " pdb=" HD1 TRP B 156 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TYR D 151 " pdb=" HD1 TYR D 151 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CZ2 TRP C 156 " pdb=" HZ2 TRP C 156 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CE1 TYR E 159 " pdb=" HE1 TYR E 159 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6045 1.90 - 3.81: 1311 3.81 - 5.71: 349 5.71 - 7.61: 122 7.61 - 9.52: 13 Bond angle restraints: 7840 Sorted by residual: angle pdb=" N GLY G 164 " pdb=" CA GLY G 164 " pdb=" C GLY G 164 " ideal model delta sigma weight residual 110.80 120.32 -9.52 1.41e+00 5.03e-01 4.56e+01 angle pdb=" N GLY F 164 " pdb=" CA GLY F 164 " pdb=" C GLY F 164 " ideal model delta sigma weight residual 110.80 120.13 -9.33 1.41e+00 5.03e-01 4.38e+01 angle pdb=" N GLY B 164 " pdb=" CA GLY B 164 " pdb=" C GLY B 164 " ideal model delta sigma weight residual 110.80 120.00 -9.20 1.41e+00 5.03e-01 4.26e+01 angle pdb=" N GLY C 164 " pdb=" CA GLY C 164 " pdb=" C GLY C 164 " ideal model delta sigma weight residual 110.80 119.69 -8.89 1.41e+00 5.03e-01 3.97e+01 angle pdb=" N GLY E 164 " pdb=" CA GLY E 164 " pdb=" C GLY E 164 " ideal model delta sigma weight residual 110.74 117.75 -7.01 1.37e+00 5.33e-01 2.62e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.08: 1750 13.08 - 26.16: 124 26.16 - 39.23: 23 39.23 - 52.31: 55 52.31 - 65.39: 88 Dihedral angle restraints: 2040 sinusoidal: 1032 harmonic: 1008 Sorted by residual: dihedral pdb=" CA LEU B 163 " pdb=" C LEU B 163 " pdb=" N GLY B 164 " pdb=" CA GLY B 164 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU F 163 " pdb=" C LEU F 163 " pdb=" N GLY F 164 " pdb=" CA GLY F 164 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA TRP C 160 " pdb=" C TRP C 160 " pdb=" N GLN C 161 " pdb=" CA GLN C 161 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.061: 173 0.061 - 0.121: 118 0.121 - 0.180: 13 0.180 - 0.240: 0 0.240 - 0.299: 8 Chirality restraints: 312 Sorted by residual: chirality pdb=" CA SER G 148 " pdb=" N SER G 148 " pdb=" C SER G 148 " pdb=" CB SER G 148 " both_signs ideal model delta sigma weight residual False 2.57 2.27 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA SER C 148 " pdb=" N SER C 148 " pdb=" C SER C 148 " pdb=" CB SER C 148 " both_signs ideal model delta sigma weight residual False 2.57 2.28 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA SER H 148 " pdb=" N SER H 148 " pdb=" C SER H 148 " pdb=" CB SER H 148 " both_signs ideal model delta sigma weight residual False 2.57 2.28 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 309 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 160 " 0.048 2.00e-02 2.50e+03 3.95e-02 6.25e+01 pdb=" CG TRP G 160 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP G 160 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP G 160 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP G 160 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP G 160 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP G 160 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 160 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 160 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP G 160 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP G 160 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TRP G 160 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP G 160 " -0.034 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 160 " 0.056 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 160 " -0.044 2.00e-02 2.50e+03 pdb=" HH2 TRP G 160 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 153 " 0.089 2.00e-02 2.50e+03 3.86e-02 5.96e+01 pdb=" CG TRP D 153 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 153 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP D 153 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 153 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP D 153 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP D 153 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 153 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 153 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 153 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TRP D 153 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TRP D 153 " -0.070 2.00e-02 2.50e+03 pdb=" HE3 TRP D 153 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 153 " 0.048 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 153 " -0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP D 153 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " -0.032 2.00e-02 2.50e+03 3.58e-02 5.12e+01 pdb=" CG TRP B 160 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP B 160 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 160 " 0.102 2.00e-02 2.50e+03 pdb=" HE3 TRP B 160 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 160 " -0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 160 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP B 160 " -0.010 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 751 2.36 - 2.92: 8880 2.92 - 3.48: 11156 3.48 - 4.04: 15822 4.04 - 4.60: 20968 Nonbonded interactions: 57577 Sorted by model distance: nonbonded pdb=" O VAL G 162 " pdb=" H LEU H 163 " model vdw 1.795 2.450 nonbonded pdb="HE21 GLN F 161 " pdb=" OE1 GLN G 161 " model vdw 1.814 2.450 nonbonded pdb=" H VAL G 162 " pdb=" O GLN H 161 " model vdw 1.816 2.450 nonbonded pdb="HE21 GLN B 161 " pdb=" OE1 GLN C 161 " model vdw 1.817 2.450 nonbonded pdb="HE21 GLN A 161 " pdb=" OE1 GLN B 161 " model vdw 1.817 2.450 ... (remaining 57572 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.090 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.037 2256 Z= 0.828 Angle : 1.743 9.519 3072 Z= 1.159 Chirality : 0.080 0.299 312 Planarity : 0.010 0.038 360 Dihedral : 10.675 48.282 712 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.92 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.013 TRP D 153 HIS 0.007 0.002 HIS G 182 PHE 0.014 0.004 PHE G 149 TYR 0.066 0.013 TYR E 151 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 3.1273 time to fit residues: 136.7029 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.155592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112217 restraints weight = 3817.474| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.37 r_work: 0.3307 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3091 rms_B_bonded: 4.20 restraints_weight: 0.1250 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9315 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2256 Z= 0.195 Angle : 0.615 4.027 3072 Z= 0.337 Chirality : 0.051 0.124 312 Planarity : 0.005 0.041 360 Dihedral : 7.182 23.731 296 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.46 % Allowed : 7.41 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 153 HIS 0.002 0.001 HIS E 182 PHE 0.003 0.001 PHE A 149 TYR 0.007 0.001 TYR B 159 ARG 0.002 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 3.3972 time to fit residues: 141.3882 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.156447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113526 restraints weight = 3793.046| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.36 r_work: 0.3323 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3104 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9303 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2256 Z= 0.157 Angle : 0.563 4.109 3072 Z= 0.303 Chirality : 0.051 0.128 312 Planarity : 0.004 0.037 360 Dihedral : 6.928 23.191 296 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 5.56 % Favored : 92.59 % 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: -1.77 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.004 0.001 PHE E 149 TYR 0.005 0.001 TYR H 159 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 3.5431 time to fit residues: 147.7290 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 0.0050 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 6.0002 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.155320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111916 restraints weight = 3798.933| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.36 r_work: 0.3304 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3084 rms_B_bonded: 4.15 restraints_weight: 0.1250 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9318 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.182 Angle : 0.585 4.289 3072 Z= 0.315 Chirality : 0.051 0.128 312 Planarity : 0.004 0.035 360 Dihedral : 7.104 25.577 296 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.85 % Allowed : 5.56 % Favored : 92.59 % 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: -1.74 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 153 HIS 0.000 0.000 HIS D 182 PHE 0.005 0.001 PHE C 149 TYR 0.005 0.001 TYR B 159 ARG 0.000 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.391 Fit side-chains REVERT: F 154 LYS cc_start: 0.9241 (mttm) cc_final: 0.9022 (mttt) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 3.7776 time to fit residues: 145.6877 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.155631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112242 restraints weight = 3891.429| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.38 r_work: 0.3310 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3095 rms_B_bonded: 4.16 restraints_weight: 0.1250 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9312 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.180 Angle : 0.586 4.537 3072 Z= 0.312 Chirality : 0.051 0.127 312 Planarity : 0.004 0.034 360 Dihedral : 7.047 25.560 296 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 5.09 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.005 0.001 PHE C 149 TYR 0.005 0.001 TYR H 159 ARG 0.001 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.391 Fit side-chains REVERT: F 154 LYS cc_start: 0.9228 (mttm) cc_final: 0.9012 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7928 time to fit residues: 142.3775 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0170 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113705 restraints weight = 3792.810| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.36 r_work: 0.3326 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3106 rms_B_bonded: 4.19 restraints_weight: 0.1250 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2256 Z= 0.163 Angle : 0.570 4.581 3072 Z= 0.299 Chirality : 0.051 0.126 312 Planarity : 0.004 0.032 360 Dihedral : 6.841 24.113 296 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 5.09 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 153 HIS 0.001 0.000 HIS E 182 PHE 0.005 0.001 PHE C 149 TYR 0.004 0.001 TYR H 159 ARG 0.001 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.381 Fit side-chains REVERT: F 154 LYS cc_start: 0.9220 (mttm) cc_final: 0.8997 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7926 time to fit residues: 142.3159 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.157656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114631 restraints weight = 3907.721| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.39 r_work: 0.3336 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3117 rms_B_bonded: 4.34 restraints_weight: 0.1250 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9284 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2256 Z= 0.149 Angle : 0.551 5.423 3072 Z= 0.287 Chirality : 0.051 0.126 312 Planarity : 0.003 0.029 360 Dihedral : 6.562 22.276 296 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 6.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 153 HIS 0.000 0.000 HIS E 182 PHE 0.004 0.001 PHE C 149 TYR 0.003 0.001 TYR F 159 ARG 0.001 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.428 Fit side-chains REVERT: F 154 LYS cc_start: 0.9224 (mttm) cc_final: 0.9001 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7641 time to fit residues: 141.2317 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.156021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113324 restraints weight = 3883.893| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.37 r_work: 0.3322 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3101 rms_B_bonded: 4.27 restraints_weight: 0.1250 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9300 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2256 Z= 0.165 Angle : 0.574 5.161 3072 Z= 0.299 Chirality : 0.051 0.127 312 Planarity : 0.003 0.032 360 Dihedral : 6.757 24.043 296 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 7.87 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 153 HIS 0.000 0.000 HIS A 182 PHE 0.005 0.001 PHE C 149 TYR 0.004 0.001 TYR H 159 ARG 0.001 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.296 Fit side-chains REVERT: F 154 LYS cc_start: 0.9237 (mttm) cc_final: 0.9010 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7640 time to fit residues: 141.3427 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.155629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112320 restraints weight = 3918.519| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.39 r_work: 0.3311 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3092 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9309 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2256 Z= 0.187 Angle : 0.596 5.935 3072 Z= 0.311 Chirality : 0.051 0.128 312 Planarity : 0.004 0.034 360 Dihedral : 6.937 25.610 296 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 8.33 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 153 HIS 0.001 0.000 HIS A 182 PHE 0.006 0.001 PHE C 149 TYR 0.004 0.001 TYR B 159 ARG 0.001 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.367 Fit side-chains REVERT: F 154 LYS cc_start: 0.9232 (mttm) cc_final: 0.9011 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7499 time to fit residues: 140.7251 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.156158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113245 restraints weight = 3838.490| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.37 r_work: 0.3324 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3104 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2256 Z= 0.163 Angle : 0.573 5.177 3072 Z= 0.299 Chirality : 0.051 0.126 312 Planarity : 0.003 0.032 360 Dihedral : 6.727 24.123 296 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 8.80 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 153 HIS 0.000 0.000 HIS A 182 PHE 0.005 0.001 PHE C 149 TYR 0.004 0.001 TYR B 159 ARG 0.000 0.000 ARG D 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.385 Fit side-chains REVERT: F 154 LYS cc_start: 0.9229 (mttm) cc_final: 0.9006 (mttt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7703 time to fit residues: 141.5963 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 overall best weight: 2.8702 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.158390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115490 restraints weight = 3912.266| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.39 r_work: 0.3350 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.3131 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2256 Z= 0.145 Angle : 0.547 4.947 3072 Z= 0.283 Chirality : 0.051 0.125 312 Planarity : 0.003 0.028 360 Dihedral : 6.405 21.629 296 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.85 % Allowed : 8.80 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 153 HIS 0.000 0.000 HIS A 182 PHE 0.004 0.001 PHE C 149 TYR 0.004 0.001 TYR F 159 ARG 0.001 0.000 ARG D 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6162.39 seconds wall clock time: 109 minutes 2.41 seconds (6542.41 seconds total)