Starting phenix.real_space_refine on Thu Jul 2 02:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.map" model { file = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2026/7ywa_34151.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 3611 2.51 5 N 998 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5808 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 608 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.39, per 1000 atoms: 0.24 Number of scatterers: 5808 At special positions: 0 Unit cell: (98.58, 79.05, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 12 15.00 Mg 2 11.99 O 1158 8.00 N 998 7.00 C 3611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 128.5 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 48.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.735A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 30 through 36 removed outlier: 5.568A pdb=" N ARG F 33 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER F 34 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 71 through 87 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 removed outlier: 4.877A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.542A pdb=" N PHE F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.505A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 312 through 328 removed outlier: 3.590A pdb=" N LEU F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 5.745A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.551A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 removed outlier: 4.922A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 218 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 328 removed outlier: 3.742A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.761A pdb=" N ALA G 91 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP G 144 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE G 93 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.761A pdb=" N ALA G 91 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP G 144 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE G 93 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL G 62 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN G 193 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE G 64 " --> pdb=" O ASN G 193 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE G 195 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY G 66 " --> pdb=" O ILE G 195 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N MET G 197 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE G 61 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL G 221 " --> pdb=" O LYS G 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS G 248 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU G 223 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL G 246 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 225 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL G 244 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG G 227 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR G 242 " --> pdb=" O ARG G 227 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY G 229 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER G 240 " --> pdb=" O GLY G 229 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL G 231 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN G 236 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA5, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.739A pdb=" N ILE F 141 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE F 192 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL F 143 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLN F 194 " --> pdb=" O VAL F 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.739A pdb=" N ILE F 141 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE F 192 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL F 143 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLN F 194 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE F 195 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY F 66 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N MET F 197 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU F 241 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA F 230 " --> pdb=" O GLY F 239 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY F 239 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS F 232 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 237 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.767A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 38 through 40 removed outlier: 4.743A pdb=" N GLU G 38 " --> pdb=" O MET G 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.262A pdb=" N TYR G 293 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 912 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: 0.65 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 1952 1.36 - 1.53: 3403 1.53 - 1.70: 489 1.70 - 1.86: 44 1.86 - 2.03: 2 Bond restraints: 5890 Sorted by residual: bond pdb=" C4 AGS F 402 " pdb=" C5 AGS F 402 " ideal model delta sigma weight residual 1.386 1.455 -0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " ideal model delta sigma weight residual 1.386 1.453 -0.067 1.00e-02 1.00e+04 4.50e+01 bond pdb=" C5 AGS F 402 " pdb=" C6 AGS F 402 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 AGS G 401 " pdb=" C6 AGS G 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" O3G AGS F 402 " pdb=" PG AGS F 402 " ideal model delta sigma weight residual 1.558 1.450 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 5885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 7823 2.71 - 5.43: 113 5.43 - 8.14: 24 8.14 - 10.86: 9 10.86 - 13.57: 1 Bond angle restraints: 7970 Sorted by residual: angle pdb=" C5 AGS F 402 " pdb=" C4 AGS F 402 " pdb=" N3 AGS F 402 " ideal model delta sigma weight residual 126.80 117.91 8.89 7.41e-01 1.82e+00 1.44e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 118.34 8.46 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " ideal model delta sigma weight residual 110.73 106.25 4.48 4.52e-01 4.89e+00 9.84e+01 angle pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " pdb=" C8 AGS G 401 " ideal model delta sigma weight residual 103.67 107.83 -4.16 4.26e-01 5.51e+00 9.54e+01 angle pdb=" C4 AGS F 402 " pdb=" C5 AGS F 402 " pdb=" N7 AGS F 402 " ideal model delta sigma weight residual 110.73 106.59 4.14 4.52e-01 4.89e+00 8.40e+01 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 3300 28.74 - 57.48: 236 57.48 - 86.22: 28 86.22 - 114.96: 1 114.96 - 143.70: 2 Dihedral angle restraints: 3567 sinusoidal: 1466 harmonic: 2101 Sorted by residual: dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.97 -143.70 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O1A AGS G 401 " pdb=" O3A AGS G 401 " pdb=" PA AGS G 401 " pdb=" PB AGS G 401 " ideal model delta sinusoidal sigma weight residual -67.73 49.39 -117.12 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA LEU G 326 " pdb=" C LEU G 326 " pdb=" N LEU G 327 " pdb=" CA LEU G 327 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 775 0.068 - 0.136: 122 0.136 - 0.204: 14 0.204 - 0.272: 1 0.272 - 0.340: 2 Chirality restraints: 914 Sorted by residual: chirality pdb=" CA ILE F 262 " pdb=" N ILE F 262 " pdb=" C ILE F 262 " pdb=" CB ILE F 262 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2' AGS G 401 " pdb=" C1' AGS G 401 " pdb=" C3' AGS G 401 " pdb=" O2' AGS G 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PRO F 101 " pdb=" N PRO F 101 " pdb=" C PRO F 101 " pdb=" CB PRO F 101 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 911 not shown) Planarity restraints: 1006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 264 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C TYR F 264 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR F 264 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY F 265 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 77 " -0.011 2.00e-02 2.50e+03 1.30e-02 4.23e+00 pdb=" CG TRP A 77 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 77 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 262 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ILE F 262 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE F 262 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU F 263 " 0.011 2.00e-02 2.50e+03 ... (remaining 1003 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 13 2.35 - 2.99: 3001 2.99 - 3.63: 8927 3.63 - 4.26: 13500 4.26 - 4.90: 22461 Nonbonded interactions: 47902 Sorted by model distance: nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 1.718 2.170 nonbonded pdb="MG MG F 403 " pdb=" O2G AGS G 401 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG F 403 " model vdw 1.978 2.170 nonbonded pdb=" O SER A 11 " pdb=" OG SER A 11 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLN F 194 " pdb=" NH1 ARG F 196 " model vdw 2.237 3.120 ... (remaining 47897 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 'F' and resid 1 through 333) selection = (chain 'G' and resid 1 through 333) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.006 0.108 5890 Z= 0.385 Angle : 0.879 13.569 7970 Z= 0.622 Chirality : 0.051 0.340 914 Planarity : 0.003 0.028 1006 Dihedral : 18.787 143.701 2223 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.85 % Allowed : 23.68 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 738 helix: 1.41 (0.28), residues: 340 sheet: 0.74 (0.43), residues: 127 loop : -1.20 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 196 TYR 0.020 0.002 TYR F 103 PHE 0.006 0.001 PHE G 260 TRP 0.036 0.003 TRP A 77 HIS 0.001 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.39 ( 5890) covalent geometry : angle 0.87918 / 0.62 ( 7970) hydrogen bonds : bond 0.13521 / 9.25 ( 315) hydrogen bonds : angle 5.90062 / 4.29 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: F 6 LYS cc_start: 0.5170 (mtpt) cc_final: 0.4962 (tppt) REVERT: F 20 GLN cc_start: 0.6916 (tt0) cc_final: 0.6448 (tt0) REVERT: F 38 GLU cc_start: 0.5771 (tt0) cc_final: 0.5326 (tp30) REVERT: F 79 VAL cc_start: 0.7221 (p) cc_final: 0.6697 (t) REVERT: F 93 ILE cc_start: 0.7529 (mm) cc_final: 0.7231 (mm) REVERT: F 169 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7232 (ttm-80) REVERT: F 198 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7704 (mtpp) REVERT: F 202 MET cc_start: 0.1797 (mmm) cc_final: 0.1009 (mtp) REVERT: F 213 ASN cc_start: 0.7975 (t0) cc_final: 0.7682 (m-40) REVERT: F 266 GLU cc_start: 0.7685 (mp0) cc_final: 0.7020 (tm-30) REVERT: G 35 MET cc_start: 0.6161 (mmt) cc_final: 0.5958 (mmt) REVERT: G 106 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6871 (mtpp) REVERT: G 110 ASP cc_start: 0.5649 (t0) cc_final: 0.4978 (m-30) REVERT: G 120 ASP cc_start: 0.7082 (m-30) cc_final: 0.6211 (t0) REVERT: G 134 ARG cc_start: 0.5317 (mtm110) cc_final: 0.4781 (mtt180) REVERT: G 162 SER cc_start: 0.7260 (m) cc_final: 0.7014 (t) REVERT: G 164 MET cc_start: 0.5781 (mmm) cc_final: 0.5098 (mmm) REVERT: G 176 ARG cc_start: 0.4899 (mmt180) cc_final: 0.3240 (mtm180) REVERT: G 177 LYS cc_start: 0.7137 (mtpp) cc_final: 0.6459 (mmtt) REVERT: G 283 LEU cc_start: 0.5871 (mt) cc_final: 0.5564 (tt) REVERT: G 310 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6198 (mtmm) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.0710 time to fit residues: 10.9629 Evaluate side-chains 92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 16 GLN F 78 GLN F 304 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.200524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.184184 restraints weight = 6559.753| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 0.82 r_work: 0.3792 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5890 Z= 0.131 Angle : 0.559 7.868 7970 Z= 0.296 Chirality : 0.043 0.147 914 Planarity : 0.003 0.021 1006 Dihedral : 12.272 133.035 871 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.90 % Allowed : 21.81 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 738 helix: 1.50 (0.27), residues: 341 sheet: 1.13 (0.44), residues: 123 loop : -1.00 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 243 TYR 0.011 0.001 TYR F 291 PHE 0.014 0.001 PHE F 260 TRP 0.022 0.002 TRP A 77 HIS 0.001 0.000 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5890) covalent geometry : angle 0.55923 / 0.30 ( 7970) hydrogen bonds : bond 0.03548 / 2.49 ( 315) hydrogen bonds : angle 4.59852 / 3.37 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: F 93 ILE cc_start: 0.7574 (mm) cc_final: 0.7324 (mm) REVERT: F 170 MET cc_start: 0.7851 (ttp) cc_final: 0.7632 (ttp) REVERT: F 202 MET cc_start: 0.1896 (mmm) cc_final: 0.1393 (ttp) REVERT: G 110 ASP cc_start: 0.6020 (t0) cc_final: 0.5476 (m-30) REVERT: G 130 ASP cc_start: 0.6378 (t0) cc_final: 0.6112 (t0) REVERT: G 176 ARG cc_start: 0.5731 (mmt180) cc_final: 0.4250 (mtm180) REVERT: G 177 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6979 (mmtt) REVERT: G 210 THR cc_start: 0.6477 (OUTLIER) cc_final: 0.6207 (p) REVERT: G 282 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6982 (mmmt) REVERT: G 322 LYS cc_start: 0.5625 (mtpt) cc_final: 0.5333 (mmmt) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.0730 time to fit residues: 9.3838 Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN G 118 GLN G 184 GLN G 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.198198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.182887 restraints weight = 6482.312| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.94 r_work: 0.3737 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5890 Z= 0.169 Angle : 0.570 8.524 7970 Z= 0.299 Chirality : 0.044 0.142 914 Planarity : 0.003 0.025 1006 Dihedral : 12.240 134.828 867 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.75 % Allowed : 20.78 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 738 helix: 1.56 (0.27), residues: 341 sheet: 0.97 (0.44), residues: 127 loop : -1.06 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 324 TYR 0.008 0.001 TYR F 291 PHE 0.014 0.001 PHE F 260 TRP 0.016 0.002 TRP A 77 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5890) covalent geometry : angle 0.56998 / 0.30 ( 7970) hydrogen bonds : bond 0.03403 / 2.35 ( 315) hydrogen bonds : angle 4.43843 / 3.25 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.6250 (m-30) cc_final: 0.6045 (m-30) REVERT: F 27 MET cc_start: 0.6969 (ptp) cc_final: 0.6452 (ttm) REVERT: F 79 VAL cc_start: 0.7831 (p) cc_final: 0.7556 (t) REVERT: F 93 ILE cc_start: 0.7633 (mm) cc_final: 0.7403 (mm) REVERT: F 166 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 202 MET cc_start: 0.1908 (mmm) cc_final: 0.1303 (mtm) REVERT: G 110 ASP cc_start: 0.5912 (t0) cc_final: 0.5333 (m-30) REVERT: G 155 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7551 (mm) REVERT: G 176 ARG cc_start: 0.5640 (mmt180) cc_final: 0.4285 (mtm110) REVERT: G 177 LYS cc_start: 0.7103 (mtpp) cc_final: 0.6822 (mmtt) REVERT: G 282 LYS cc_start: 0.7316 (mmtt) cc_final: 0.7092 (mmmt) outliers start: 22 outliers final: 13 residues processed: 101 average time/residue: 0.0590 time to fit residues: 7.7017 Evaluate side-chains 87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN G 7 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.178934 restraints weight = 6543.107| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.06 r_work: 0.3687 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5890 Z= 0.235 Angle : 0.627 7.962 7970 Z= 0.328 Chirality : 0.047 0.150 914 Planarity : 0.004 0.033 1006 Dihedral : 12.534 140.671 867 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.11 % Allowed : 20.27 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 738 helix: 1.23 (0.27), residues: 343 sheet: 0.75 (0.44), residues: 127 loop : -1.12 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 324 TYR 0.008 0.002 TYR G 291 PHE 0.017 0.002 PHE F 260 TRP 0.015 0.002 TRP A 77 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 5890) covalent geometry : angle 0.62744 / 0.33 ( 7970) hydrogen bonds : bond 0.03719 / 2.52 ( 315) hydrogen bonds : angle 4.64331 / 3.40 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.6827 (mp0) cc_final: 0.6352 (mp0) REVERT: F 27 MET cc_start: 0.7138 (ptp) cc_final: 0.6482 (ttp) REVERT: F 93 ILE cc_start: 0.7791 (mm) cc_final: 0.7497 (mm) REVERT: F 166 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7427 (tt) REVERT: F 202 MET cc_start: 0.2625 (mmm) cc_final: 0.1477 (mtm) REVERT: F 270 PHE cc_start: 0.6468 (t80) cc_final: 0.6237 (t80) REVERT: G 176 ARG cc_start: 0.5798 (mmt180) cc_final: 0.4190 (mtm110) REVERT: G 177 LYS cc_start: 0.7216 (mtpp) cc_final: 0.6806 (mmtt) REVERT: G 282 LYS cc_start: 0.7455 (mmtt) cc_final: 0.7168 (mmmt) REVERT: G 310 LYS cc_start: 0.6831 (ttmm) cc_final: 0.6393 (mtmm) outliers start: 30 outliers final: 24 residues processed: 99 average time/residue: 0.0565 time to fit residues: 7.3993 Evaluate side-chains 93 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.195881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177304 restraints weight = 6600.888| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 0.93 r_work: 0.3676 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5890 Z= 0.170 Angle : 0.545 6.936 7970 Z= 0.290 Chirality : 0.044 0.140 914 Planarity : 0.003 0.031 1006 Dihedral : 12.238 135.124 867 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.43 % Allowed : 21.81 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.30), residues: 738 helix: 1.34 (0.27), residues: 343 sheet: 0.79 (0.44), residues: 123 loop : -1.07 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 324 TYR 0.007 0.001 TYR F 65 PHE 0.013 0.001 PHE F 260 TRP 0.012 0.001 TRP A 77 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 5890) covalent geometry : angle 0.54527 / 0.29 ( 7970) hydrogen bonds : bond 0.03316 / 2.27 ( 315) hydrogen bonds : angle 4.48401 / 3.27 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7031 (mp0) cc_final: 0.6627 (mp0) REVERT: F 27 MET cc_start: 0.6931 (ptp) cc_final: 0.6561 (ttp) REVERT: F 68 GLU cc_start: 0.7160 (pm20) cc_final: 0.6219 (tt0) REVERT: F 93 ILE cc_start: 0.7684 (mm) cc_final: 0.7392 (mm) REVERT: F 166 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7361 (tt) REVERT: F 203 PHE cc_start: 0.3563 (OUTLIER) cc_final: 0.2513 (m-10) REVERT: F 270 PHE cc_start: 0.6258 (t80) cc_final: 0.6031 (t80) REVERT: G 176 ARG cc_start: 0.5572 (mmt180) cc_final: 0.4220 (mtm110) REVERT: G 177 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6773 (mmtt) outliers start: 26 outliers final: 21 residues processed: 92 average time/residue: 0.0603 time to fit residues: 7.3282 Evaluate side-chains 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.195523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178831 restraints weight = 6588.481| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 0.86 r_work: 0.3690 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5890 Z= 0.175 Angle : 0.555 7.324 7970 Z= 0.293 Chirality : 0.044 0.141 914 Planarity : 0.003 0.031 1006 Dihedral : 12.159 135.275 867 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.62 % Allowed : 19.76 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.30), residues: 738 helix: 1.33 (0.27), residues: 343 sheet: 0.73 (0.44), residues: 123 loop : -1.11 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 2 TYR 0.016 0.002 TYR G 271 PHE 0.012 0.001 PHE F 260 TRP 0.012 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 5890) covalent geometry : angle 0.55526 / 0.29 ( 7970) hydrogen bonds : bond 0.03283 / 2.25 ( 315) hydrogen bonds : angle 4.48086 / 3.26 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.133 Fit side-chains REVERT: A 72 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: F 27 MET cc_start: 0.7126 (ptp) cc_final: 0.6618 (ttp) REVERT: F 68 GLU cc_start: 0.7158 (pm20) cc_final: 0.6204 (tt0) REVERT: F 93 ILE cc_start: 0.7726 (mm) cc_final: 0.7398 (mm) REVERT: F 130 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: F 166 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7325 (tt) REVERT: F 202 MET cc_start: 0.2756 (mmm) cc_final: 0.1731 (mtp) REVERT: F 203 PHE cc_start: 0.3470 (OUTLIER) cc_final: 0.2365 (m-80) REVERT: F 270 PHE cc_start: 0.6309 (t80) cc_final: 0.6106 (t80) REVERT: G 176 ARG cc_start: 0.5730 (mmt180) cc_final: 0.4206 (mtm110) REVERT: G 177 LYS cc_start: 0.7172 (mtpp) cc_final: 0.6772 (mmtt) outliers start: 33 outliers final: 22 residues processed: 95 average time/residue: 0.0672 time to fit residues: 8.3646 Evaluate side-chains 91 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN G 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.192669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174845 restraints weight = 6622.987| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 0.91 r_work: 0.3682 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5890 Z= 0.167 Angle : 0.547 7.174 7970 Z= 0.290 Chirality : 0.044 0.138 914 Planarity : 0.003 0.032 1006 Dihedral : 12.073 134.420 867 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.79 % Allowed : 20.10 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 738 helix: 1.39 (0.28), residues: 343 sheet: 0.75 (0.45), residues: 123 loop : -1.08 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 196 TYR 0.013 0.001 TYR G 271 PHE 0.012 0.002 PHE F 191 TRP 0.011 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5890) covalent geometry : angle 0.54696 / 0.29 ( 7970) hydrogen bonds : bond 0.03225 / 2.22 ( 315) hydrogen bonds : angle 4.44833 / 3.23 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.124 Fit side-chains REVERT: A 72 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: F 27 MET cc_start: 0.7228 (ptp) cc_final: 0.6685 (ttp) REVERT: F 68 GLU cc_start: 0.7143 (pm20) cc_final: 0.6187 (tt0) REVERT: F 93 ILE cc_start: 0.7715 (mm) cc_final: 0.7406 (mm) REVERT: F 130 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: F 166 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7412 (tt) REVERT: F 202 MET cc_start: 0.2760 (mmm) cc_final: 0.1726 (mtp) REVERT: F 203 PHE cc_start: 0.3212 (OUTLIER) cc_final: 0.2090 (m-80) REVERT: F 270 PHE cc_start: 0.6292 (t80) cc_final: 0.6090 (t80) REVERT: G 8 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5180 (tptp) REVERT: G 176 ARG cc_start: 0.5951 (mmt180) cc_final: 0.4112 (mtm110) REVERT: G 177 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6798 (mmtt) outliers start: 34 outliers final: 25 residues processed: 94 average time/residue: 0.0580 time to fit residues: 7.2561 Evaluate side-chains 95 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.192908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.176637 restraints weight = 6526.790| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 0.83 r_work: 0.3711 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5890 Z= 0.181 Angle : 0.558 7.398 7970 Z= 0.295 Chirality : 0.044 0.139 914 Planarity : 0.003 0.032 1006 Dihedral : 12.080 135.339 867 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.45 % Allowed : 19.76 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.30), residues: 738 helix: 1.35 (0.27), residues: 343 sheet: 0.77 (0.45), residues: 123 loop : -1.10 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.012 0.001 TYR G 271 PHE 0.011 0.002 PHE F 260 TRP 0.011 0.001 TRP A 77 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 5890) covalent geometry : angle 0.55779 / 0.29 ( 7970) hydrogen bonds : bond 0.03272 / 2.24 ( 315) hydrogen bonds : angle 4.45196 / 3.23 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.151 Fit side-chains REVERT: A 72 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: F 27 MET cc_start: 0.7189 (ptp) cc_final: 0.6685 (ttp) REVERT: F 68 GLU cc_start: 0.7145 (pm20) cc_final: 0.6203 (tt0) REVERT: F 130 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: F 166 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7387 (tt) REVERT: F 203 PHE cc_start: 0.3198 (OUTLIER) cc_final: 0.2092 (m-80) REVERT: G 8 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5145 (tptp) REVERT: G 176 ARG cc_start: 0.5913 (mmt180) cc_final: 0.4139 (mtm110) REVERT: G 177 LYS cc_start: 0.7179 (mtpp) cc_final: 0.6790 (mmtt) outliers start: 32 outliers final: 25 residues processed: 91 average time/residue: 0.0627 time to fit residues: 7.4894 Evaluate side-chains 92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.195474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.179429 restraints weight = 6583.100| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.83 r_work: 0.3742 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5890 Z= 0.140 Angle : 0.519 6.800 7970 Z= 0.279 Chirality : 0.043 0.136 914 Planarity : 0.003 0.031 1006 Dihedral : 11.861 131.087 867 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.77 % Allowed : 20.44 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.31), residues: 738 helix: 1.47 (0.28), residues: 343 sheet: 0.84 (0.45), residues: 123 loop : -1.03 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 169 TYR 0.012 0.001 TYR G 271 PHE 0.009 0.001 PHE F 260 TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5890) covalent geometry : angle 0.51936 / 0.28 ( 7970) hydrogen bonds : bond 0.03051 / 2.11 ( 315) hydrogen bonds : angle 4.37094 / 3.15 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.306 Fit side-chains REVERT: A 70 THR cc_start: 0.8190 (m) cc_final: 0.7597 (t) REVERT: A 72 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: F 27 MET cc_start: 0.7155 (ptp) cc_final: 0.6661 (ttp) REVERT: F 68 GLU cc_start: 0.7105 (pm20) cc_final: 0.6137 (tt0) REVERT: F 93 ILE cc_start: 0.7641 (mm) cc_final: 0.7324 (mm) REVERT: F 130 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: F 166 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7221 (tt) REVERT: F 203 PHE cc_start: 0.3235 (OUTLIER) cc_final: 0.2114 (m-80) REVERT: G 8 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5217 (tptp) REVERT: G 176 ARG cc_start: 0.5897 (mmt180) cc_final: 0.4227 (mtm110) REVERT: G 177 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6787 (mmtt) outliers start: 28 outliers final: 21 residues processed: 85 average time/residue: 0.0758 time to fit residues: 8.6121 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 0.0010 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.198348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.181503 restraints weight = 6601.264| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.02 r_work: 0.3695 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5890 Z= 0.113 Angle : 0.496 6.422 7970 Z= 0.268 Chirality : 0.042 0.130 914 Planarity : 0.003 0.030 1006 Dihedral : 11.636 126.994 867 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.75 % Allowed : 21.12 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.31), residues: 738 helix: 1.59 (0.28), residues: 343 sheet: 0.89 (0.46), residues: 123 loop : -0.99 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 33 TYR 0.012 0.001 TYR G 271 PHE 0.008 0.001 PHE F 260 TRP 0.008 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 5890) covalent geometry : angle 0.49601 / 0.27 ( 7970) hydrogen bonds : bond 0.02895 / 2.01 ( 315) hydrogen bonds : angle 4.28562 / 3.08 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.156 Fit side-chains REVERT: A 70 THR cc_start: 0.8144 (m) cc_final: 0.7577 (t) REVERT: A 72 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: F 27 MET cc_start: 0.7156 (ptp) cc_final: 0.6646 (ttp) REVERT: F 68 GLU cc_start: 0.7106 (pm20) cc_final: 0.6130 (tt0) REVERT: F 93 ILE cc_start: 0.7588 (mm) cc_final: 0.7282 (mm) REVERT: F 166 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7210 (tt) REVERT: G 130 ASP cc_start: 0.6325 (t0) cc_final: 0.6116 (t0) REVERT: G 176 ARG cc_start: 0.5905 (mmt180) cc_final: 0.4136 (mtm110) REVERT: G 177 LYS cc_start: 0.7195 (mtpp) cc_final: 0.6792 (mttt) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.0752 time to fit residues: 8.1821 Evaluate side-chains 81 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177995 restraints weight = 6559.981| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 0.82 r_work: 0.3718 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5890 Z= 0.167 Angle : 0.555 10.070 7970 Z= 0.292 Chirality : 0.044 0.133 914 Planarity : 0.003 0.032 1006 Dihedral : 11.867 133.421 867 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.92 % Allowed : 20.78 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.31), residues: 738 helix: 1.47 (0.28), residues: 343 sheet: 0.91 (0.46), residues: 123 loop : -1.06 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 169 TYR 0.010 0.001 TYR G 271 PHE 0.014 0.002 PHE F 191 TRP 0.010 0.001 TRP A 77 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 5890) covalent geometry : angle 0.55472 / 0.29 ( 7970) hydrogen bonds : bond 0.03142 / 2.16 ( 315) hydrogen bonds : angle 4.35118 / 3.13 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.32 seconds wall clock time: 21 minutes 21.35 seconds (1281.35 seconds total)