Starting phenix.real_space_refine on Tue Feb 11 04:51:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsv_61784/02_2025/9jsv_61784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsv_61784/02_2025/9jsv_61784.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/9jsv_61784/02_2025/9jsv_61784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsv_61784/02_2025/9jsv_61784.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsv_61784/02_2025/9jsv_61784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsv_61784/02_2025/9jsv_61784.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= 0.006 sd= 0.061 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-5592/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: 2.61, per 1000 atoms: 0.61 Number of scatterers: 4248 At special positions: 0 Unit cell: (85.2048, 83.448, 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: 1.05 Conformation dependent library (CDL) restraints added in 267.7 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, 60.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 163 removed outlier: 6.571A pdb=" N VAL A 150 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TRP B 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 152 " --> pdb=" O TRP B 153 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR B 155 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LYS A 154 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N GLY B 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N TRP A 156 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N TYR B 159 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN A 158 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLN B 161 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP A 160 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 163 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 162 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C 155 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP B 156 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY C 157 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B 158 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR C 159 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR D 155 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TRP C 156 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY D 157 " --> pdb=" O TRP C 156 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN C 158 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.960A 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: 7.981A pdb=" N SER A 168 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N SER B 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N LEU A 170 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER B 168 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER C 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N LEU B 170 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N SER C 168 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER D 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LEU C 170 " --> pdb=" O SER D 171 " (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: 6.502A pdb=" N ARG A 176 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU B 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET A 178 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG B 176 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU C 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET B 178 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 176 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU D 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET C 178 " --> pdb=" O LEU D 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 153 removed outlier: 6.614A pdb=" N VAL E 150 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TRP F 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL E 152 " --> pdb=" O TRP F 153 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL F 150 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TRP G 153 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F 152 " --> pdb=" O TRP G 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 156 through 163 removed outlier: 6.937A pdb=" N GLY F 157 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN E 158 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR F 159 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY G 157 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN F 158 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR G 159 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY H 157 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN G 158 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 6.852A 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: 7.971A pdb=" N SER E 168 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER F 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N LEU E 170 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER F 168 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER G 171 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N LEU F 170 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER G 168 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER H 171 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 8.876A 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: 6.506A pdb=" N ARG E 176 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU F 179 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 178 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG F 176 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU G 179 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET F 178 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG G 176 " --> pdb=" O ALA H 177 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU H 179 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 6.663A 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: 1.25 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: 0.94 - 1.12: 2104 1.12 - 1.29: 288 1.29 - 1.47: 947 1.47 - 1.64: 973 1.64 - 1.82: 16 Bond restraints: 4328 Sorted by residual: bond pdb=" CD2 TYR G 159 " pdb=" HD2 TYR G 159 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU F 179 " pdb=" H LEU F 179 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ILE C 172 " pdb=" H ILE C 172 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N MET A 178 " pdb=" H MET A 178 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N TYR F 159 " pdb=" H TYR F 159 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 4323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 5435 1.65 - 3.29: 1626 3.29 - 4.94: 415 4.94 - 6.59: 243 6.59 - 8.23: 25 Bond angle restraints: 7744 Sorted by residual: angle pdb=" C GLY E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta sigma weight residual 119.90 124.25 -4.35 1.02e+00 9.61e-01 1.82e+01 angle pdb=" CB HIS G 182 " pdb=" CG HIS G 182 " pdb=" CD2 HIS G 182 " ideal model delta sigma weight residual 131.20 125.72 5.48 1.30e+00 5.92e-01 1.78e+01 angle pdb=" OE1 GLN F 161 " pdb=" CD GLN F 161 " pdb=" NE2 GLN F 161 " ideal model delta sigma weight residual 122.60 118.40 4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" C GLY H 165 " pdb=" N PRO H 166 " pdb=" CA PRO H 166 " ideal model delta sigma weight residual 119.78 124.06 -4.28 1.03e+00 9.43e-01 1.73e+01 angle pdb=" CB HIS H 182 " pdb=" CG HIS H 182 " pdb=" CD2 HIS H 182 " ideal model delta sigma weight residual 131.20 125.84 5.36 1.30e+00 5.92e-01 1.70e+01 ... (remaining 7739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.10: 1729 13.10 - 26.21: 110 26.21 - 39.31: 28 39.31 - 52.42: 55 52.42 - 65.52: 94 Dihedral angle restraints: 2016 sinusoidal: 1016 harmonic: 1000 Sorted by residual: dihedral pdb=" CA TRP B 160 " pdb=" C TRP B 160 " pdb=" N GLN B 161 " pdb=" CA GLN B 161 " ideal model delta harmonic sigma weight residual 180.00 164.79 15.21 0 5.00e+00 4.00e-02 9.26e+00 dihedral pdb=" C TYR C 159 " pdb=" N TYR C 159 " pdb=" CA TYR C 159 " pdb=" CB TYR C 159 " ideal model delta harmonic sigma weight residual -122.60 -129.83 7.23 0 2.50e+00 1.60e-01 8.35e+00 dihedral pdb=" CA TRP D 160 " pdb=" C TRP D 160 " pdb=" N GLN D 161 " pdb=" CA GLN D 161 " ideal model delta harmonic sigma weight residual 180.00 165.56 14.44 0 5.00e+00 4.00e-02 8.34e+00 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 114 0.044 - 0.087: 99 0.087 - 0.130: 63 0.130 - 0.174: 27 0.174 - 0.217: 9 Chirality restraints: 312 Sorted by residual: chirality pdb=" CA TYR E 159 " pdb=" N TYR E 159 " pdb=" C TYR E 159 " pdb=" CB TYR E 159 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR D 155 " pdb=" CA THR D 155 " pdb=" OG1 THR D 155 " pdb=" CG2 THR D 155 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA TYR A 159 " pdb=" N TYR A 159 " pdb=" C TYR A 159 " pdb=" CB TYR A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 309 not shown) Planarity restraints: 608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 160 " 0.040 2.00e-02 2.50e+03 3.56e-02 5.08e+01 pdb=" CG TRP C 160 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 160 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 160 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP C 160 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP C 160 " -0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP C 160 " -0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 160 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 160 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 160 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 TRP C 160 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP C 160 " 0.034 2.00e-02 2.50e+03 pdb=" HE3 TRP C 160 " -0.026 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 160 " -0.020 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 160 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP C 160 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 160 " 0.013 2.00e-02 2.50e+03 3.28e-02 4.29e+01 pdb=" CG TRP D 160 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP D 160 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP D 160 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP D 160 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP D 160 " -0.045 2.00e-02 2.50e+03 pdb=" CE3 TRP D 160 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 160 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 160 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP D 160 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP D 160 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 TRP D 160 " 0.053 2.00e-02 2.50e+03 pdb=" HE3 TRP D 160 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 160 " -0.025 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 160 " 0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP D 160 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.036 2.00e-02 2.50e+03 3.20e-02 4.11e+01 pdb=" CG TRP B 160 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " -0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " -0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 160 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 TRP B 160 " 0.039 2.00e-02 2.50e+03 pdb=" HE3 TRP B 160 " -0.017 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 160 " -0.010 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 160 " 0.042 2.00e-02 2.50e+03 pdb=" HH2 TRP B 160 " 0.041 2.00e-02 2.50e+03 ... (remaining 605 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 686 2.32 - 2.89: 8600 2.89 - 3.46: 10713 3.46 - 4.03: 15652 4.03 - 4.60: 20637 Nonbonded interactions: 56288 Sorted by model distance: nonbonded pdb=" O SER F 168 " pdb=" H GLY G 169 " model vdw 1.752 2.450 nonbonded pdb=" O SER G 168 " pdb=" H GLY H 169 " model vdw 1.769 2.450 nonbonded pdb=" O SER B 168 " pdb=" H GLY C 169 " model vdw 1.775 2.450 nonbonded pdb="HE21 GLN B 161 " pdb=" OE1 GLN C 161 " model vdw 1.775 2.450 nonbonded pdb=" O SER C 168 " pdb=" H GLY D 169 " model vdw 1.788 2.450 ... (remaining 56283 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: 0.050 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.013 0.038 2224 Z= 0.816 Angle : 1.775 6.533 3032 Z= 1.192 Chirality : 0.085 0.217 312 Planarity : 0.008 0.030 352 Dihedral : 11.539 53.934 704 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.39 % Allowed : 0.93 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.013 TRP B 160 HIS 0.004 0.002 HIS E 182 PHE 0.016 0.007 PHE H 149 TYR 0.058 0.011 TYR A 159 ARG 0.003 0.001 ARG B 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 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: E 178 MET cc_start: 0.7913 (mtm) cc_final: 0.7584 (mtp) REVERT: F 178 MET cc_start: 0.7876 (mtm) cc_final: 0.7523 (mtp) REVERT: G 178 MET cc_start: 0.7627 (mtm) cc_final: 0.7410 (mtp) REVERT: D 178 MET cc_start: 0.7232 (mtm) cc_final: 0.6963 (mtp) REVERT: H 170 LEU cc_start: 0.6935 (tt) cc_final: 0.6716 (tp) REVERT: H 178 MET cc_start: 0.7496 (mtm) cc_final: 0.7102 (mtp) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 2.2274 time to fit residues: 77.6030 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 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: 10.0000 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.142210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119530 restraints weight = 4686.660| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.22 r_work: 0.3454 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3249 rms_B_bonded: 4.68 restraints_weight: 0.1250 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9357 moved from start: 0.2257 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= 0.197 Angle : 0.545 4.194 3032 Z= 0.303 Chirality : 0.054 0.135 312 Planarity : 0.003 0.018 352 Dihedral : 4.014 12.051 288 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 153 HIS 0.002 0.000 HIS E 182 PHE 0.003 0.001 PHE G 149 TYR 0.010 0.002 TYR C 151 ARG 0.001 0.000 ARG A 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 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.363 Fit side-chains REVERT: B 181 THR cc_start: 0.7828 (m) cc_final: 0.7437 (p) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 3.1630 time to fit residues: 67.7632 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.141711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119128 restraints weight = 4605.131| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.21 r_work: 0.3442 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.3239 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9362 moved from start: 0.2658 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= 0.175 Angle : 0.513 4.178 3032 Z= 0.288 Chirality : 0.053 0.138 312 Planarity : 0.003 0.020 352 Dihedral : 3.853 10.909 288 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 153 HIS 0.002 0.001 HIS B 182 PHE 0.003 0.001 PHE H 149 TYR 0.010 0.002 TYR C 151 ARG 0.002 0.000 ARG G 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 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 3.6195 time to fit residues: 66.3577 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.141923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119173 restraints weight = 4646.583| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.24 r_work: 0.3447 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3244 rms_B_bonded: 4.70 restraints_weight: 0.1250 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9355 moved from start: 0.2749 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= 0.169 Angle : 0.487 4.035 3032 Z= 0.272 Chirality : 0.053 0.138 312 Planarity : 0.003 0.020 352 Dihedral : 3.716 10.941 288 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 153 HIS 0.001 0.000 HIS E 182 PHE 0.002 0.000 PHE G 149 TYR 0.009 0.001 TYR C 151 ARG 0.001 0.000 ARG G 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.6071 time to fit residues: 69.8117 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.144002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121470 restraints weight = 4769.315| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.24 r_work: 0.3478 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.3280 rms_B_bonded: 4.73 restraints_weight: 0.1250 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9328 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2224 Z= 0.109 Angle : 0.417 4.233 3032 Z= 0.236 Chirality : 0.051 0.136 312 Planarity : 0.003 0.021 352 Dihedral : 3.307 9.220 288 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -0.79 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 153 HIS 0.000 0.000 HIS A 182 PHE 0.001 0.000 PHE G 149 TYR 0.009 0.001 TYR F 159 ARG 0.001 0.000 ARG G 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 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.358 Fit side-chains REVERT: B 181 THR cc_start: 0.7895 (m) cc_final: 0.7544 (p) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 3.4114 time to fit residues: 69.5997 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 overall best weight: 5.1986 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.142374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119581 restraints weight = 4643.844| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.22 r_work: 0.3447 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3245 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9355 moved from start: 0.2871 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= 0.163 Angle : 0.475 3.986 3032 Z= 0.266 Chirality : 0.053 0.141 312 Planarity : 0.002 0.019 352 Dihedral : 3.583 10.555 288 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -0.90 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 153 HIS 0.001 0.000 HIS D 182 PHE 0.002 0.000 PHE C 149 TYR 0.008 0.002 TYR C 151 ARG 0.001 0.000 ARG C 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.4661 time to fit residues: 67.0961 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.143581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121150 restraints weight = 4668.374| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.20 r_work: 0.3467 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.3264 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9339 moved from start: 0.2934 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= 0.136 Angle : 0.443 4.081 3032 Z= 0.249 Chirality : 0.052 0.139 312 Planarity : 0.002 0.021 352 Dihedral : 3.406 9.805 288 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -0.83 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.001 0.000 PHE G 149 TYR 0.008 0.001 TYR F 159 ARG 0.001 0.000 ARG E 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 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.362 Fit side-chains REVERT: B 181 THR cc_start: 0.7919 (m) cc_final: 0.7571 (p) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 3.3031 time to fit residues: 67.4156 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.141595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118809 restraints weight = 4555.259| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.22 r_work: 0.3437 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.3232 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9362 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2224 Z= 0.201 Angle : 0.507 4.063 3032 Z= 0.285 Chirality : 0.053 0.142 312 Planarity : 0.003 0.019 352 Dihedral : 3.688 11.018 288 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.004 0.001 PHE G 149 TYR 0.009 0.002 TYR C 151 ARG 0.001 0.000 ARG B 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.4764 time to fit residues: 67.3059 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.142573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119780 restraints weight = 4689.840| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.23 r_work: 0.3451 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.3248 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9351 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2224 Z= 0.156 Angle : 0.470 4.027 3032 Z= 0.264 Chirality : 0.052 0.142 312 Planarity : 0.003 0.020 352 Dihedral : 3.556 10.323 288 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 256 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 0.002 0.000 PHE G 149 TYR 0.008 0.001 TYR C 151 ARG 0.001 0.000 ARG E 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.5076 time to fit residues: 67.8983 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.142728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120004 restraints weight = 4646.013| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.22 r_work: 0.3454 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3251 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9349 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2224 Z= 0.148 Angle : 0.459 4.029 3032 Z= 0.258 Chirality : 0.052 0.137 312 Planarity : 0.002 0.020 352 Dihedral : 3.515 10.161 288 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.002 0.000 PHE G 149 TYR 0.008 0.001 TYR C 151 ARG 0.000 0.000 ARG E 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.392 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.5094 time to fit residues: 68.0428 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.142285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119518 restraints weight = 4627.329| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.22 r_work: 0.3448 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3243 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9354 moved from start: 0.2931 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= 0.168 Angle : 0.477 4.020 3032 Z= 0.268 Chirality : 0.053 0.143 312 Planarity : 0.003 0.020 352 Dihedral : 3.566 10.380 288 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.45), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 153 HIS 0.001 0.000 HIS B 182 PHE 0.002 0.000 PHE G 149 TYR 0.009 0.002 TYR C 151 ARG 0.001 0.000 ARG C 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.47 seconds wall clock time: 92 minutes 3.46 seconds (5523.46 seconds total)