Starting phenix.real_space_refine on Thu Nov 14 05:23:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsx_61786/11_2024/9jsx_61786.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= 0.003 sd= 0.018 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 1424 2.51 5 N 360 2.21 5 O 352 1.98 5 H 2104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "F" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 531 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 2.97, per 1000 atoms: 0.70 Number of scatterers: 4248 At special positions: 0 Unit cell: (84.3264, 85.2048, 44.7984, 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 352 8.00 N 360 7.00 C 1424 6.00 H 2104 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: 1.01 Conformation dependent library (CDL) restraints added in 309.8 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 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 7 sheets defined 0.0% alpha, 59.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 163 removed outlier: 6.569A pdb=" N VAL A 150 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TRP B 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 152 " --> pdb=" O TRP B 153 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR B 155 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS A 154 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N GLY B 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N TRP A 156 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N TYR B 159 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN A 158 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN B 161 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP A 160 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU B 163 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 162 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 155 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TRP B 156 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY C 157 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN B 158 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C 159 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 154 " --> pdb=" O TRP D 153 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR D 155 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP C 156 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY D 157 " --> pdb=" O TRP C 156 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN C 158 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR D 159 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172 removed outlier: 10.154A pdb=" N VAL A 167 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU B 170 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 169 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE B 172 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 171 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER B 168 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N SER C 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LEU B 170 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER C 168 " --> pdb=" O GLY D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.491A pdb=" N ARG B 176 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU C 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET B 178 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 176 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU D 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET C 178 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 153 removed outlier: 6.546A pdb=" N VAL E 150 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TRP F 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 152 " --> pdb=" O TRP F 153 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL F 150 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TRP G 153 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 152 " --> pdb=" O TRP G 153 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL G 150 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TRP H 153 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 152 " --> pdb=" O TRP H 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 156 through 163 removed outlier: 6.961A pdb=" N GLY F 157 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN E 158 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR F 159 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY G 157 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN F 158 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR G 159 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY H 157 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN G 158 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR H 159 " --> pdb=" O GLN G 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 167 through 172 removed outlier: 7.843A pdb=" N SER E 168 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER F 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU E 170 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N SER F 168 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER G 171 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N LEU F 170 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER G 168 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER H 171 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU G 170 " --> pdb=" O SER H 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 175 through 179 removed outlier: 6.626A pdb=" N ARG E 176 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU F 179 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET E 178 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 176 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU G 179 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET F 178 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG G 176 " --> pdb=" O ALA H 177 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU H 179 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET G 178 " --> pdb=" O LEU H 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 31 hydrogen bonds defined for protein. 93 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: 1.33 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 483 1.05 - 1.24: 1908 1.24 - 1.43: 769 1.43 - 1.62: 1152 1.62 - 1.82: 16 Bond restraints: 4328 Sorted by residual: bond pdb=" N TRP F 156 " pdb=" H TRP F 156 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY G 157 " pdb=" H GLY G 157 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CZ3 TRP C 156 " pdb=" HZ3 TRP C 156 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL E 162 " pdb=" H VAL E 162 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL B 152 " pdb=" H VAL B 152 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 4323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 5475 1.72 - 3.44: 1602 3.44 - 5.16: 407 5.16 - 6.88: 243 6.88 - 8.60: 17 Bond angle restraints: 7744 Sorted by residual: angle pdb=" C GLY C 165 " pdb=" N PRO C 166 " pdb=" CA PRO C 166 " ideal model delta sigma weight residual 119.90 124.89 -4.99 1.02e+00 9.61e-01 2.39e+01 angle pdb=" OE1 GLN F 161 " pdb=" CD GLN F 161 " pdb=" NE2 GLN F 161 " ideal model delta sigma weight residual 122.60 118.23 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CB HIS H 182 " pdb=" CG HIS H 182 " pdb=" CD2 HIS H 182 " ideal model delta sigma weight residual 131.20 125.57 5.63 1.30e+00 5.92e-01 1.87e+01 angle pdb=" CB HIS G 182 " pdb=" CG HIS G 182 " pdb=" CD2 HIS G 182 " ideal model delta sigma weight residual 131.20 125.60 5.60 1.30e+00 5.92e-01 1.86e+01 angle pdb=" C GLY G 165 " pdb=" N PRO G 166 " pdb=" CA PRO G 166 " ideal model delta sigma weight residual 119.76 124.19 -4.43 1.03e+00 9.43e-01 1.85e+01 ... (remaining 7739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 1741 12.97 - 25.94: 103 25.94 - 38.91: 36 38.91 - 51.88: 54 51.88 - 64.85: 82 Dihedral angle restraints: 2016 sinusoidal: 1016 harmonic: 1000 Sorted by residual: dihedral pdb=" CA SER D 171 " pdb=" C SER D 171 " pdb=" N ILE D 172 " pdb=" CA ILE D 172 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" C SER B 168 " pdb=" N SER B 168 " pdb=" CA SER B 168 " pdb=" CB SER B 168 " ideal model delta harmonic sigma weight residual -122.60 -136.96 14.36 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" CA SER C 171 " pdb=" C SER C 171 " pdb=" N ILE C 172 " pdb=" CA ILE C 172 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 230 0.105 - 0.210: 76 0.210 - 0.314: 3 0.314 - 0.419: 2 0.419 - 0.524: 1 Chirality restraints: 312 Sorted by residual: chirality pdb=" CA SER B 168 " pdb=" N SER B 168 " pdb=" C SER B 168 " pdb=" CB SER B 168 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" CA SER C 168 " pdb=" N SER C 168 " pdb=" C SER C 168 " pdb=" CB SER C 168 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA SER A 168 " pdb=" N SER A 168 " pdb=" C SER A 168 " pdb=" CB SER A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 309 not shown) Planarity restraints: 608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 160 " 0.020 2.00e-02 2.50e+03 3.05e-02 3.71e+01 pdb=" CG TRP C 160 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP C 160 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 160 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP C 160 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP C 160 " -0.053 2.00e-02 2.50e+03 pdb=" CE3 TRP C 160 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 160 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 160 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP C 160 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 TRP C 160 " 0.031 2.00e-02 2.50e+03 pdb=" HE3 TRP C 160 " -0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 160 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 160 " 0.042 2.00e-02 2.50e+03 pdb=" HH2 TRP C 160 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.051 2.00e-02 2.50e+03 2.99e-02 3.57e+01 pdb=" CG TRP B 160 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " -0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " -0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 160 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TRP B 160 " 0.035 2.00e-02 2.50e+03 pdb=" HE3 TRP B 160 " -0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 160 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 160 " 0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP B 160 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 160 " 0.058 2.00e-02 2.50e+03 2.62e-02 2.74e+01 pdb=" CG TRP D 160 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP D 160 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 160 " -0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP D 160 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP D 160 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP D 160 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 160 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 160 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 160 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP D 160 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP D 160 " 0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP D 160 " -0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 160 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 160 " 0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP D 160 " 0.043 2.00e-02 2.50e+03 ... (remaining 605 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 321 2.19 - 2.80: 6833 2.80 - 3.40: 10548 3.40 - 4.00: 15710 4.00 - 4.60: 20942 Nonbonded interactions: 54354 Sorted by model distance: nonbonded pdb=" HG SER B 168 " pdb=" O VAL C 167 " model vdw 1.593 2.450 nonbonded pdb=" HG SER C 168 " pdb=" O VAL D 167 " model vdw 1.623 2.450 nonbonded pdb=" HG SER A 168 " pdb=" O VAL B 167 " model vdw 1.644 2.450 nonbonded pdb=" HB3 SER C 171 " pdb=" H ILE D 172 " model vdw 1.741 2.270 nonbonded pdb="HE21 GLN F 161 " pdb=" OE1 GLN G 161 " model vdw 1.800 2.450 ... (remaining 54349 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: 0.040 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: 0.030 Set scattering table: 0.050 Process input model: 14.330 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 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 : 0.014 0.129 2224 Z= 0.911 Angle : 1.877 8.227 3032 Z= 1.247 Chirality : 0.099 0.524 312 Planarity : 0.008 0.033 352 Dihedral : 11.583 55.614 704 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.85 % Allowed : 1.39 % Favored : 96.76 % Cbeta Deviations : 1.34 % 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: -0.91 (0.46), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.011 TRP D 160 HIS 0.004 0.002 HIS C 182 PHE 0.013 0.005 PHE H 149 TYR 0.060 0.014 TYR A 159 ARG 0.003 0.001 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 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: 4 poor density : 38 time to evaluate : 0.399 Fit side-chains REVERT: C 154 LYS cc_start: 0.5776 (mttm) cc_final: 0.5564 (mttt) REVERT: D 178 MET cc_start: 0.6729 (mtm) cc_final: 0.6473 (mtp) outliers start: 4 outliers final: 0 residues processed: 38 average time/residue: 2.0913 time to fit residues: 81.4601 Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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: 0.5733 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2224 Z= 0.234 Angle : 0.620 4.523 3032 Z= 0.348 Chirality : 0.054 0.143 312 Planarity : 0.003 0.018 352 Dihedral : 4.599 21.237 288 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -1.12 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 153 HIS 0.002 0.001 HIS C 182 PHE 0.006 0.001 PHE G 149 TYR 0.011 0.002 TYR F 151 ARG 0.002 0.001 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.387 Fit side-chains REVERT: D 178 MET cc_start: 0.6853 (mtm) cc_final: 0.6556 (mtp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 2.5746 time to fit residues: 68.5187 Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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: 0.5759 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2224 Z= 0.188 Angle : 0.544 4.447 3032 Z= 0.301 Chirality : 0.053 0.138 312 Planarity : 0.003 0.015 352 Dihedral : 4.043 16.362 288 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -1.38 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 153 HIS 0.003 0.001 HIS C 182 PHE 0.004 0.001 PHE A 149 TYR 0.009 0.002 TYR F 151 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.424 Fit side-chains REVERT: D 178 MET cc_start: 0.6859 (mtm) cc_final: 0.6546 (mtp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 2.2304 time to fit residues: 68.6553 Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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: 0.5778 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2224 Z= 0.186 Angle : 0.535 4.372 3032 Z= 0.295 Chirality : 0.053 0.144 312 Planarity : 0.003 0.018 352 Dihedral : 3.933 15.828 288 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 153 HIS 0.002 0.001 HIS C 182 PHE 0.004 0.001 PHE C 149 TYR 0.009 0.002 TYR F 151 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.369 Fit side-chains REVERT: D 178 MET cc_start: 0.6841 (mtm) cc_final: 0.6561 (mtp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 2.1838 time to fit residues: 62.8744 Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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: 0.5792 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2224 Z= 0.176 Angle : 0.513 4.304 3032 Z= 0.284 Chirality : 0.053 0.136 312 Planarity : 0.003 0.016 352 Dihedral : 3.797 14.040 288 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: -1.33 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 153 HIS 0.002 0.001 HIS C 182 PHE 0.004 0.001 PHE A 149 TYR 0.008 0.002 TYR F 151 ARG 0.001 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.320 Fit side-chains REVERT: D 178 MET cc_start: 0.6910 (mtm) cc_final: 0.6598 (mtp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 2.0009 time to fit residues: 57.4162 Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.5821 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2224 Z= 0.213 Angle : 0.569 4.502 3032 Z= 0.314 Chirality : 0.054 0.143 312 Planarity : 0.003 0.020 352 Dihedral : 4.088 15.476 288 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -1.36 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 153 HIS 0.003 0.001 HIS C 182 PHE 0.005 0.001 PHE A 149 TYR 0.010 0.002 TYR F 151 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.387 Fit side-chains REVERT: D 178 MET cc_start: 0.6915 (mtm) cc_final: 0.6582 (mtp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 2.1178 time to fit residues: 63.1334 Evaluate side-chains 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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: 0.5825 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2224 Z= 0.179 Angle : 0.513 4.314 3032 Z= 0.284 Chirality : 0.053 0.138 312 Planarity : 0.003 0.022 352 Dihedral : 3.775 13.692 288 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -1.32 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 153 HIS 0.002 0.001 HIS C 182 PHE 0.004 0.001 PHE A 149 TYR 0.008 0.002 TYR F 159 ARG 0.001 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.377 Fit side-chains REVERT: D 178 MET cc_start: 0.6965 (mtm) cc_final: 0.6629 (mtp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 2.1963 time to fit residues: 63.1319 Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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: 0.5833 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2224 Z= 0.165 Angle : 0.494 4.265 3032 Z= 0.273 Chirality : 0.052 0.136 312 Planarity : 0.003 0.023 352 Dihedral : 3.694 12.124 288 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.46 % Allowed : 4.17 % Favored : 95.37 % 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: -1.30 (0.43), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 153 HIS 0.002 0.001 HIS C 182 PHE 0.003 0.001 PHE A 149 TYR 0.008 0.002 TYR F 159 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.358 Fit side-chains REVERT: D 178 MET cc_start: 0.6972 (mtm) cc_final: 0.6583 (mtp) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 2.2483 time to fit residues: 64.6523 Evaluate side-chains 27 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.4064 ------------------------------------------------------------------------------- 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: 0.5834 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2224 Z= 0.145 Angle : 0.465 4.094 3032 Z= 0.255 Chirality : 0.052 0.135 312 Planarity : 0.003 0.025 352 Dihedral : 3.503 10.770 288 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -1.26 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 153 HIS 0.001 0.000 HIS C 182 PHE 0.002 0.000 PHE A 149 TYR 0.009 0.001 TYR F 159 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.425 Fit side-chains REVERT: D 178 MET cc_start: 0.6914 (mtm) cc_final: 0.6595 (mtp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 2.2497 time to fit residues: 66.9493 Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.5858 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2224 Z= 0.195 Angle : 0.536 4.422 3032 Z= 0.296 Chirality : 0.053 0.138 312 Planarity : 0.003 0.016 352 Dihedral : 3.844 13.069 288 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -1.32 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 153 HIS 0.002 0.001 HIS C 182 PHE 0.004 0.001 PHE C 149 TYR 0.010 0.002 TYR F 151 ARG 0.001 0.000 ARG G 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.340 Fit side-chains REVERT: D 178 MET cc_start: 0.6919 (mtm) cc_final: 0.6547 (mtp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 2.1811 time to fit residues: 62.7615 Evaluate side-chains 28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.161346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144515 restraints weight = 3445.637| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 0.59 r_work: 0.3644 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.3410 rms_B_bonded: 3.28 restraints_weight: 0.1250 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2224 Z= 0.208 Angle : 0.553 4.410 3032 Z= 0.306 Chirality : 0.054 0.141 312 Planarity : 0.003 0.016 352 Dihedral : 3.950 13.972 288 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -1.34 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 153 HIS 0.002 0.001 HIS C 182 PHE 0.004 0.001 PHE A 149 TYR 0.009 0.002 TYR F 151 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: 2350.61 seconds wall clock time: 45 minutes 26.27 seconds (2726.27 seconds total)