Starting phenix.real_space_refine on Tue Aug 4 18:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ywa_34151/08_2026/7ywa_34151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ywa_34151/08_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_34151/08_2026/7ywa_34151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ywa_34151/08_2026/7ywa_34151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ywa_34151/08_2026/7ywa_34151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ywa_34151/08_2026/7ywa_34151.map" model { file = "/net/cci-nas-00/data/ceres_data/7ywa_34151/08_2026/7ywa_34151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ywa_34151/08_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-2.2rc3-6140/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: 1.49, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 143.1 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: 0.35 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: 0.99 Time building geometry restraints manager: 0.49 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- 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 0.87920 / 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 : 0.215 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: 0.0891 time to fit residues: 13.6573 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 : 0.261 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.200572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.183997 restraints weight = 6556.552| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 0.83 r_work: 0.3791 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5890 Z= 0.130 Angle : 0.561 7.723 7970 Z= 0.296 Chirality : 0.043 0.144 914 Planarity : 0.003 0.021 1006 Dihedral : 12.272 132.747 871 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.07 % Allowed : 21.47 % 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: 1.49 (0.27), residues: 341 sheet: 1.14 (0.44), residues: 123 loop : -1.01 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 243 TYR 0.012 0.001 TYR F 264 PHE 0.013 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 0.00284 / 0.13 ( 5890) covalent geometry : angle 0.56120 / 0.30 ( 7970) hydrogen bonds : bond 0.03482 / 2.45 ( 315) hydrogen bonds : angle 4.58932 / 3.36 ( 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 111 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: F 93 ILE cc_start: 0.7568 (mm) cc_final: 0.7347 (mm) REVERT: F 170 MET cc_start: 0.7836 (ttp) cc_final: 0.7617 (ttp) REVERT: F 202 MET cc_start: 0.1940 (mmm) cc_final: 0.1407 (ttp) REVERT: G 110 ASP cc_start: 0.6029 (t0) cc_final: 0.5474 (m-30) REVERT: G 130 ASP cc_start: 0.6427 (t0) cc_final: 0.6150 (t0) REVERT: G 176 ARG cc_start: 0.5741 (mmt180) cc_final: 0.4204 (mtm110) REVERT: G 177 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6999 (mmtt) REVERT: G 210 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6211 (p) REVERT: G 282 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6996 (mmmt) REVERT: G 322 LYS cc_start: 0.5692 (mtpt) cc_final: 0.5387 (mmmt) outliers start: 18 outliers final: 8 residues processed: 106 average time/residue: 0.0899 time to fit residues: 11.8249 Evaluate side-chains 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 3.9990 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: 0.9980 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.201190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.183328 restraints weight = 6437.978| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 0.78 r_work: 0.3746 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5890 Z= 0.140 Angle : 0.539 8.445 7970 Z= 0.284 Chirality : 0.043 0.139 914 Planarity : 0.003 0.023 1006 Dihedral : 12.114 132.174 867 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.75 % Allowed : 20.10 % Favored : 76.15 % 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: 0.89 (0.30), residues: 738 helix: 1.62 (0.27), residues: 341 sheet: 1.14 (0.44), residues: 123 loop : -1.00 (0.36), residues: 274 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 0.012 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 0.00314 / 0.14 ( 5890) covalent geometry : angle 0.53888 / 0.28 ( 7970) hydrogen bonds : bond 0.03244 / 2.26 ( 315) hydrogen bonds : angle 4.36134 / 3.19 ( 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 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: F 27 MET cc_start: 0.6884 (ptp) cc_final: 0.6411 (ttm) REVERT: F 79 VAL cc_start: 0.7804 (p) cc_final: 0.7505 (t) REVERT: F 93 ILE cc_start: 0.7521 (mm) cc_final: 0.7302 (mm) REVERT: F 202 MET cc_start: 0.1839 (mmm) cc_final: 0.1277 (mtm) REVERT: G 110 ASP cc_start: 0.5837 (t0) cc_final: 0.5312 (m-30) REVERT: G 155 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7511 (mm) REVERT: G 176 ARG cc_start: 0.5589 (mmt180) cc_final: 0.4297 (mtm110) REVERT: G 177 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6929 (mmtt) REVERT: G 282 LYS cc_start: 0.7281 (mmtt) cc_final: 0.7067 (mmmt) outliers start: 22 outliers final: 13 residues processed: 100 average time/residue: 0.0828 time to fit residues: 10.6568 Evaluate side-chains 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.201520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.185816 restraints weight = 6485.959| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.80 r_work: 0.3792 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5890 Z= 0.112 Angle : 0.491 6.652 7970 Z= 0.264 Chirality : 0.042 0.136 914 Planarity : 0.003 0.025 1006 Dihedral : 11.881 127.476 867 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 21.98 % 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: 1.03 (0.31), residues: 738 helix: 1.72 (0.28), residues: 343 sheet: 1.23 (0.44), residues: 123 loop : -0.93 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 33 TYR 0.007 0.001 TYR F 293 PHE 0.009 0.001 PHE F 260 TRP 0.013 0.001 TRP A 77 HIS 0.002 0.000 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 5890) covalent geometry : angle 0.49101 / 0.26 ( 7970) hydrogen bonds : bond 0.02980 / 2.07 ( 315) hydrogen bonds : angle 4.22735 / 3.09 ( 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 95 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: F 18 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6642 (mm-30) REVERT: F 27 MET cc_start: 0.6968 (ptp) cc_final: 0.6471 (ttm) REVERT: F 79 VAL cc_start: 0.7828 (p) cc_final: 0.7546 (t) REVERT: F 93 ILE cc_start: 0.7519 (mm) cc_final: 0.7271 (mm) REVERT: F 270 PHE cc_start: 0.6165 (t80) cc_final: 0.5904 (t80) REVERT: G 110 ASP cc_start: 0.5795 (t0) cc_final: 0.5284 (m-30) REVERT: G 155 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7536 (mm) REVERT: G 176 ARG cc_start: 0.5714 (mmt180) cc_final: 0.4127 (mtm110) REVERT: G 177 LYS cc_start: 0.7053 (mtpp) cc_final: 0.6838 (mttt) REVERT: G 310 LYS cc_start: 0.6754 (ttmm) cc_final: 0.6380 (mtmm) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.0838 time to fit residues: 9.8659 Evaluate side-chains 85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 242 THR 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 146 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.197167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178900 restraints weight = 6605.686| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 0.89 r_work: 0.3702 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2275 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= 0.185 Angle : 0.558 7.351 7970 Z= 0.293 Chirality : 0.045 0.139 914 Planarity : 0.003 0.029 1006 Dihedral : 12.114 135.767 867 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.60 % Allowed : 20.27 % 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: 0.86 (0.30), residues: 738 helix: 1.59 (0.27), residues: 343 sheet: 1.02 (0.44), residues: 127 loop : -1.01 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 324 TYR 0.006 0.001 TYR F 65 PHE 0.012 0.002 PHE F 191 TRP 0.013 0.002 TRP A 77 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 5890) covalent geometry : angle 0.55810 / 0.29 ( 7970) hydrogen bonds : bond 0.03295 / 2.25 ( 315) hydrogen bonds : angle 4.32498 / 3.16 ( 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 100 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.6786 (mp0) cc_final: 0.6487 (mp0) REVERT: F 27 MET cc_start: 0.7047 (ptp) cc_final: 0.6520 (ttp) REVERT: F 93 ILE cc_start: 0.7644 (mm) cc_final: 0.7379 (mm) REVERT: F 270 PHE cc_start: 0.6306 (t80) cc_final: 0.6088 (t80) REVERT: G 155 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7522 (mm) REVERT: G 176 ARG cc_start: 0.5939 (mmt180) cc_final: 0.4251 (mtm110) REVERT: G 177 LYS cc_start: 0.7105 (mtpp) cc_final: 0.6782 (mmtt) REVERT: G 310 LYS cc_start: 0.6780 (ttmm) cc_final: 0.6374 (mtmm) outliers start: 27 outliers final: 22 residues processed: 94 average time/residue: 0.0822 time to fit residues: 10.0670 Evaluate side-chains 92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 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 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.196695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.180661 restraints weight = 6588.718| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.04 r_work: 0.3733 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2449 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= 0.182 Angle : 0.553 7.297 7970 Z= 0.292 Chirality : 0.044 0.143 914 Planarity : 0.003 0.029 1006 Dihedral : 12.125 135.869 867 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.09 % Allowed : 20.61 % 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: 0.76 (0.30), residues: 738 helix: 1.48 (0.27), residues: 343 sheet: 1.04 (0.44), residues: 123 loop : -1.01 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 27 TYR 0.006 0.001 TYR F 65 PHE 0.010 0.002 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 0.00421 / 0.18 ( 5890) covalent geometry : angle 0.55330 / 0.29 ( 7970) hydrogen bonds : bond 0.03290 / 2.25 ( 315) hydrogen bonds : angle 4.36175 / 3.18 ( 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 95 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.210 Fit side-chains REVERT: A 72 GLU cc_start: 0.6902 (mp0) cc_final: 0.6693 (mp0) REVERT: F 27 MET cc_start: 0.6767 (ptp) cc_final: 0.6512 (ttp) REVERT: F 68 GLU cc_start: 0.7178 (pm20) cc_final: 0.6196 (tt0) REVERT: F 93 ILE cc_start: 0.7615 (mm) cc_final: 0.7335 (mm) REVERT: F 270 PHE cc_start: 0.6171 (t80) cc_final: 0.5955 (t80) REVERT: G 176 ARG cc_start: 0.5580 (mmt180) cc_final: 0.4274 (mtm110) outliers start: 24 outliers final: 21 residues processed: 92 average time/residue: 0.0724 time to fit residues: 8.6783 Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.199553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.183796 restraints weight = 6567.011| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 0.81 r_work: 0.3794 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5890 Z= 0.109 Angle : 0.489 5.933 7970 Z= 0.265 Chirality : 0.042 0.134 914 Planarity : 0.003 0.041 1006 Dihedral : 11.703 127.331 867 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.26 % Allowed : 20.95 % 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: 1.00 (0.31), residues: 738 helix: 1.69 (0.28), residues: 343 sheet: 1.14 (0.45), residues: 123 loop : -0.90 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.006 0.001 TYR F 65 PHE 0.008 0.001 PHE F 260 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 0.00243 / 0.11 ( 5890) covalent geometry : angle 0.48922 / 0.26 ( 7970) hydrogen bonds : bond 0.02900 / 2.02 ( 315) hydrogen bonds : angle 4.22041 / 3.07 ( 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 100 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.138 Fit side-chains REVERT: A 72 GLU cc_start: 0.7086 (mp0) cc_final: 0.6795 (mp0) REVERT: F 27 MET cc_start: 0.6947 (ptp) cc_final: 0.6513 (ttp) REVERT: F 68 GLU cc_start: 0.7091 (pm20) cc_final: 0.6142 (tt0) REVERT: F 93 ILE cc_start: 0.7517 (mm) cc_final: 0.7255 (mm) REVERT: G 155 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7486 (mm) REVERT: G 176 ARG cc_start: 0.5782 (mmt180) cc_final: 0.4112 (mtm110) REVERT: G 208 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7865 (t) REVERT: G 310 LYS cc_start: 0.6822 (ttmm) cc_final: 0.6482 (mtmm) outliers start: 25 outliers final: 17 residues processed: 96 average time/residue: 0.0780 time to fit residues: 9.6678 Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 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 201 VAL Chi-restraints excluded: chain G residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 0.3980 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.198157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.181358 restraints weight = 6493.619| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 0.83 r_work: 0.3767 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5890 Z= 0.139 Angle : 0.508 6.710 7970 Z= 0.271 Chirality : 0.043 0.136 914 Planarity : 0.003 0.048 1006 Dihedral : 11.707 129.721 867 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.58 % Allowed : 21.12 % 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: 0.98 (0.31), residues: 738 helix: 1.69 (0.28), residues: 343 sheet: 1.12 (0.45), residues: 123 loop : -0.94 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.005 0.001 TYR F 65 PHE 0.009 0.001 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 0.00318 / 0.14 ( 5890) covalent geometry : angle 0.50777 / 0.27 ( 7970) hydrogen bonds : bond 0.02982 / 2.06 ( 315) hydrogen bonds : angle 4.21735 / 3.07 ( 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 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.216 Fit side-chains REVERT: A 72 GLU cc_start: 0.7006 (mp0) cc_final: 0.6633 (mp0) REVERT: F 27 MET cc_start: 0.6986 (ptp) cc_final: 0.6530 (ttp) REVERT: F 68 GLU cc_start: 0.7115 (pm20) cc_final: 0.6156 (tt0) REVERT: F 93 ILE cc_start: 0.7546 (mm) cc_final: 0.7265 (mm) REVERT: G 155 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7458 (mm) REVERT: G 176 ARG cc_start: 0.5743 (mmt180) cc_final: 0.4108 (mtm110) REVERT: G 310 LYS cc_start: 0.6790 (ttmm) cc_final: 0.6461 (mtmm) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.0682 time to fit residues: 7.7908 Evaluate side-chains 83 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 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: 5.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.199124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.183224 restraints weight = 6579.531| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.82 r_work: 0.3783 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5890 Z= 0.123 Angle : 0.500 6.469 7970 Z= 0.267 Chirality : 0.042 0.135 914 Planarity : 0.003 0.029 1006 Dihedral : 11.565 128.248 867 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.90 % Allowed : 21.64 % 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: 1.04 (0.31), residues: 738 helix: 1.75 (0.28), residues: 343 sheet: 1.17 (0.46), residues: 123 loop : -0.93 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 27 TYR 0.005 0.001 TYR F 65 PHE 0.008 0.001 PHE F 260 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 0.00282 / 0.12 ( 5890) covalent geometry : angle 0.49958 / 0.27 ( 7970) hydrogen bonds : bond 0.02903 / 2.01 ( 315) hydrogen bonds : angle 4.16209 / 3.01 ( 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 85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.196 Fit side-chains REVERT: A 72 GLU cc_start: 0.7081 (mp0) cc_final: 0.6754 (mp0) REVERT: F 27 MET cc_start: 0.7047 (ptp) cc_final: 0.6559 (ttp) REVERT: F 68 GLU cc_start: 0.7065 (pm20) cc_final: 0.6150 (tt0) REVERT: F 93 ILE cc_start: 0.7517 (mm) cc_final: 0.7219 (mm) REVERT: F 202 MET cc_start: 0.2499 (mmm) cc_final: 0.1387 (ptm) REVERT: G 155 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7442 (mm) REVERT: G 176 ARG cc_start: 0.5745 (mmt180) cc_final: 0.4175 (mtm110) REVERT: G 310 LYS cc_start: 0.6797 (ttmm) cc_final: 0.6459 (mtmm) REVERT: G 325 GLU cc_start: 0.4960 (tm-30) cc_final: 0.4608 (tt0) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.0722 time to fit residues: 7.8685 Evaluate side-chains 81 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.199085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.182755 restraints weight = 6625.729| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 0.86 r_work: 0.3788 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5890 Z= 0.121 Angle : 0.493 6.538 7970 Z= 0.265 Chirality : 0.042 0.133 914 Planarity : 0.003 0.054 1006 Dihedral : 11.484 127.595 867 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.07 % Allowed : 21.47 % 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: 1.05 (0.31), residues: 738 helix: 1.73 (0.28), residues: 343 sheet: 1.20 (0.46), residues: 123 loop : -0.90 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 27 TYR 0.009 0.001 TYR F 291 PHE 0.012 0.001 PHE F 191 TRP 0.010 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5890) covalent geometry : angle 0.49276 / 0.26 ( 7970) hydrogen bonds : bond 0.02913 / 2.01 ( 315) hydrogen bonds : angle 4.13461 / 2.99 ( 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 82 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: F 27 MET cc_start: 0.7082 (ptp) cc_final: 0.6568 (ttp) REVERT: F 68 GLU cc_start: 0.7078 (pm20) cc_final: 0.6156 (tt0) REVERT: F 93 ILE cc_start: 0.7487 (mm) cc_final: 0.7215 (mm) REVERT: F 202 MET cc_start: 0.2498 (mmm) cc_final: 0.1448 (ptm) REVERT: G 155 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7405 (mm) REVERT: G 176 ARG cc_start: 0.5690 (mmt180) cc_final: 0.4100 (mtm110) REVERT: G 310 LYS cc_start: 0.6836 (ttmm) cc_final: 0.6459 (mtmm) REVERT: G 325 GLU cc_start: 0.4887 (tm-30) cc_final: 0.4577 (tt0) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.0704 time to fit residues: 7.4152 Evaluate side-chains 82 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 201 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.201093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.185234 restraints weight = 6504.837| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 0.80 r_work: 0.3807 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.002 0.029 5890 Z= 0.104 Angle : 0.486 6.106 7970 Z= 0.261 Chirality : 0.042 0.130 914 Planarity : 0.003 0.051 1006 Dihedral : 11.261 124.061 867 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.90 % Allowed : 21.98 % 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: 1.12 (0.31), residues: 738 helix: 1.76 (0.28), residues: 343 sheet: 1.28 (0.46), residues: 123 loop : -0.84 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 27 TYR 0.007 0.001 TYR F 291 PHE 0.008 0.001 PHE F 191 TRP 0.010 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 5890) covalent geometry : angle 0.48563 / 0.26 ( 7970) hydrogen bonds : bond 0.02834 / 1.96 ( 315) hydrogen bonds : angle 4.09427 / 2.96 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.86 seconds wall clock time: 24 minutes 10.80 seconds (1450.80 seconds total)