Starting phenix.real_space_refine on Wed Aug 5 03:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.cif Found real_map, /net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.map" model { file = "/net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22bk_68153/08_2026/22bk_68153.cif" } resolution = 2.7 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 38 5.16 5 C 5366 2.51 5 N 1356 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 8089 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2016 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 Chain: "C" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2027 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2021 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain breaks: 2 Chain: "B" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2021 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.25 Number of scatterers: 8089 At special positions: 0 Unit cell: (82.368, 115.128, 123.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 38 16.00 O 1325 8.00 N 1356 7.00 C 5366 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: 0.65 Conformation dependent library (CDL) restraints added in 468.1 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.757A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 115 removed outlier: 3.750A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.571A pdb=" N GLY A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.933A pdb=" N LEU A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.645A pdb=" N ARG A 198 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 199 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.701A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.846A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.506A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 87 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.668A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 3.880A pdb=" N GLY C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 5.190A pdb=" N CYS C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG C 153 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 155 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 4.276A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 removed outlier: 3.616A pdb=" N ILE C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.659A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 removed outlier: 6.621A pdb=" N ARG C 214 " --> pdb=" O MET C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 306 removed outlier: 3.873A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 327 Processing helix chain 'D' and resid 104 through 117 removed outlier: 4.334A pdb=" N LEU D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 143 removed outlier: 4.136A pdb=" N LEU D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D 125 " --> pdb=" O TRP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 177 removed outlier: 3.860A pdb=" N TRP D 155 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 186 through 193 removed outlier: 4.245A pdb=" N ARG D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.047A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 257 through 282 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 326 through 345 removed outlier: 3.603A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 366 Processing helix chain 'B' and resid 104 through 117 removed outlier: 4.334A pdb=" N LEU B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 143 removed outlier: 4.136A pdb=" N LEU B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR B 125 " --> pdb=" O TRP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 177 removed outlier: 3.859A pdb=" N TRP B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 186 through 193 removed outlier: 4.246A pdb=" N ARG B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.047A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 257 through 282 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 326 through 345 removed outlier: 3.603A pdb=" N LEU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 366 586 hydrogen bonds defined for protein. 1725 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: 0.85 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2439 1.34 - 1.46: 1964 1.46 - 1.58: 3838 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 8293 Sorted by residual: bond pdb=" N ILE D 107 " pdb=" CA ILE D 107 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.38e+00 bond pdb=" N ILE B 107 " pdb=" CA ILE B 107 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.28e+00 bond pdb=" N ARG B 106 " pdb=" CA ARG B 106 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.21e+00 bond pdb=" N ARG D 106 " pdb=" CA ARG D 106 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.99e+00 bond pdb=" N ASP B 202 " pdb=" CA ASP B 202 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.85e+00 ... (remaining 8288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 10764 1.02 - 2.04: 336 2.04 - 3.06: 106 3.06 - 4.08: 10 4.08 - 5.10: 10 Bond angle restraints: 11226 Sorted by residual: angle pdb=" CA ASP B 202 " pdb=" CB ASP B 202 " pdb=" CG ASP B 202 " ideal model delta sigma weight residual 112.60 115.63 -3.03 1.00e+00 1.00e+00 9.20e+00 angle pdb=" N ASP B 202 " pdb=" CA ASP B 202 " pdb=" C ASP B 202 " ideal model delta sigma weight residual 111.07 107.86 3.21 1.07e+00 8.73e-01 9.01e+00 angle pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" O ARG A 210 " ideal model delta sigma weight residual 120.82 117.69 3.13 1.05e+00 9.07e-01 8.88e+00 angle pdb=" O ILE B 107 " pdb=" C ILE B 107 " pdb=" N GLN B 108 " ideal model delta sigma weight residual 121.83 124.49 -2.66 1.03e+00 9.43e-01 6.68e+00 angle pdb=" CA ARG D 106 " pdb=" C ARG D 106 " pdb=" O ARG D 106 " ideal model delta sigma weight residual 120.82 118.11 2.71 1.05e+00 9.07e-01 6.67e+00 ... (remaining 11221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4357 17.07 - 34.14: 320 34.14 - 51.21: 68 51.21 - 68.29: 13 68.29 - 85.36: 8 Dihedral angle restraints: 4766 sinusoidal: 1885 harmonic: 2881 Sorted by residual: dihedral pdb=" CD ARG B 227 " pdb=" NE ARG B 227 " pdb=" CZ ARG B 227 " pdb=" NH1 ARG B 227 " ideal model delta sinusoidal sigma weight residual 0.00 85.36 -85.36 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CD ARG D 227 " pdb=" NE ARG D 227 " pdb=" CZ ARG D 227 " pdb=" NH1 ARG D 227 " ideal model delta sinusoidal sigma weight residual 0.00 85.35 -85.35 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CD ARG A 210 " pdb=" NE ARG A 210 " pdb=" CZ ARG A 210 " pdb=" NH1 ARG A 210 " ideal model delta sinusoidal sigma weight residual 0.00 -75.46 75.46 1 1.00e+01 1.00e-02 7.19e+01 ... (remaining 4763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 932 0.038 - 0.077: 272 0.077 - 0.115: 41 0.115 - 0.153: 16 0.153 - 0.192: 2 Chirality restraints: 1263 Sorted by residual: chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ILE D 107 " pdb=" N ILE D 107 " pdb=" C ILE D 107 " pdb=" CB ILE D 107 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CG LEU B 235 " pdb=" CB LEU B 235 " pdb=" CD1 LEU B 235 " pdb=" CD2 LEU B 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1260 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 227 " -1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG D 227 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 227 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 227 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 227 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 227 " -1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG B 227 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 227 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 227 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 227 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " 1.068 9.50e-02 1.11e+02 4.79e-01 1.38e+02 pdb=" NE ARG A 210 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " 0.021 2.00e-02 2.50e+03 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 2061 2.80 - 3.38: 9142 3.38 - 3.97: 14974 3.97 - 4.55: 21157 4.55 - 5.14: 29827 Nonbonded interactions: 77161 Sorted by model distance: nonbonded pdb=" OH TYR C 280 " pdb=" OG1 THR B 313 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 280 " pdb=" OG1 THR D 313 " model vdw 2.254 3.040 nonbonded pdb=" O SER C 110 " pdb=" OG SER C 113 " model vdw 2.303 3.040 nonbonded pdb=" O LEU C 272 " pdb=" OG1 THR C 276 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" OH TYR D 319 " model vdw 2.304 3.040 ... (remaining 77156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 71 through 901) } ncs_group { reference = (chain 'B' and resid 103 through 367) selection = chain 'D' } 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: 2.000 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 : 0.003 0.035 8293 Z= 0.172 Angle : 0.473 5.101 11226 Z= 0.289 Chirality : 0.038 0.192 1263 Planarity : 0.032 0.494 1348 Dihedral : 13.106 85.358 2920 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.48 % Allowed : 1.20 % Favored : 98.32 % 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: 0.94 (0.26), residues: 979 helix: 0.64 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 1.12 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 227 TYR 0.008 0.001 TYR B 319 PHE 0.011 0.001 PHE B 231 TRP 0.009 0.001 TRP D 187 HIS 0.002 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 ( 8293) covalent geometry : angle 0.47317 / 0.29 (11226) hydrogen bonds : bond 0.23403 / 15.48 ( 586) hydrogen bonds : angle 7.22722 / 5.32 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6245 (tmm160) cc_final: 0.5824 (ppt170) REVERT: A 105 SER cc_start: 0.7396 (m) cc_final: 0.7153 (m) REVERT: A 202 PHE cc_start: 0.4791 (m-80) cc_final: 0.4456 (p90) REVERT: A 214 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6340 (ttm110) REVERT: A 223 SER cc_start: 0.8523 (t) cc_final: 0.8216 (p) REVERT: C 78 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6112 (mm-40) REVERT: C 142 PHE cc_start: 0.7275 (m-10) cc_final: 0.6977 (m-10) REVERT: C 242 CYS cc_start: 0.7844 (t) cc_final: 0.7625 (m) REVERT: C 255 LYS cc_start: 0.8206 (tptp) cc_final: 0.7957 (tptp) REVERT: D 240 MET cc_start: 0.8083 (ttm) cc_final: 0.7792 (tpt) REVERT: D 252 SER cc_start: 0.8271 (t) cc_final: 0.7942 (p) REVERT: D 265 TRP cc_start: 0.7657 (m-10) cc_final: 0.7450 (m100) REVERT: D 284 LYS cc_start: 0.7647 (pttt) cc_final: 0.6616 (tptp) REVERT: D 296 MET cc_start: 0.5666 (mpp) cc_final: 0.5337 (mpt) REVERT: D 301 GLU cc_start: 0.7613 (pt0) cc_final: 0.7125 (pt0) REVERT: D 339 ILE cc_start: 0.8286 (mt) cc_final: 0.7903 (mm) REVERT: B 237 MET cc_start: 0.8433 (mmm) cc_final: 0.8116 (mmm) REVERT: B 262 ILE cc_start: 0.8647 (mt) cc_final: 0.8425 (mm) REVERT: B 284 LYS cc_start: 0.7529 (pttt) cc_final: 0.7123 (pttp) REVERT: B 296 MET cc_start: 0.4191 (mpp) cc_final: 0.3096 (tpt) REVERT: B 358 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7656 (tptt) outliers start: 4 outliers final: 2 residues processed: 191 average time/residue: 0.6662 time to fit residues: 133.5787 Evaluate side-chains 129 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain B residue 330 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.203685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114309 restraints weight = 8761.321| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.44 r_work: 0.3179 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8293 Z= 0.181 Angle : 0.559 8.902 11226 Z= 0.297 Chirality : 0.040 0.159 1263 Planarity : 0.006 0.080 1348 Dihedral : 4.693 53.846 1112 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.12 % Allowed : 11.76 % Favored : 85.11 % 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: 2.11 (0.26), residues: 979 helix: 1.52 (0.18), residues: 765 sheet: None (None), residues: 0 loop : 1.31 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 117 TYR 0.012 0.002 TYR A 74 PHE 0.017 0.002 PHE D 204 TRP 0.011 0.001 TRP B 187 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8293) covalent geometry : angle 0.55918 / 0.30 (11226) hydrogen bonds : bond 0.05048 / 3.32 ( 586) hydrogen bonds : angle 4.28929 / 3.13 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6078 (tmm160) cc_final: 0.5565 (ppt170) REVERT: A 101 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6342 (mp) REVERT: A 105 SER cc_start: 0.7037 (m) cc_final: 0.6835 (m) REVERT: A 210 ARG cc_start: 0.5972 (mtp-110) cc_final: 0.4531 (tmt170) REVERT: A 214 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6667 (ttm110) REVERT: A 236 TRP cc_start: 0.7529 (m-10) cc_final: 0.7129 (m100) REVERT: C 142 PHE cc_start: 0.7569 (m-10) cc_final: 0.7271 (m-80) REVERT: C 214 ARG cc_start: 0.7416 (mpt180) cc_final: 0.6482 (mtp85) REVERT: C 242 CYS cc_start: 0.8640 (t) cc_final: 0.8276 (m) REVERT: D 117 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6313 (pmm150) REVERT: D 243 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6660 (ptp-170) REVERT: D 284 LYS cc_start: 0.7571 (pttt) cc_final: 0.6626 (tptp) REVERT: D 296 MET cc_start: 0.5767 (mpp) cc_final: 0.5451 (mpt) REVERT: D 298 GLU cc_start: 0.6987 (tp30) cc_final: 0.6628 (tp30) REVERT: D 301 GLU cc_start: 0.7923 (pt0) cc_final: 0.7486 (pt0) REVERT: D 358 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7258 (tppt) REVERT: B 145 PHE cc_start: 0.6269 (m-80) cc_final: 0.6062 (m-80) REVERT: B 233 GLN cc_start: 0.5895 (OUTLIER) cc_final: 0.5636 (mp10) REVERT: B 237 MET cc_start: 0.8498 (mmm) cc_final: 0.8249 (mmm) REVERT: B 262 ILE cc_start: 0.8918 (mt) cc_final: 0.8709 (mm) REVERT: B 284 LYS cc_start: 0.7609 (pttt) cc_final: 0.7315 (pttp) REVERT: B 296 MET cc_start: 0.4312 (mpp) cc_final: 0.3250 (tpt) outliers start: 26 outliers final: 10 residues processed: 148 average time/residue: 0.6506 time to fit residues: 101.3901 Evaluate side-chains 130 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 330 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.205597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117114 restraints weight = 8609.888| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.41 r_work: 0.3153 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8293 Z= 0.123 Angle : 0.484 8.976 11226 Z= 0.254 Chirality : 0.037 0.139 1263 Planarity : 0.004 0.035 1348 Dihedral : 4.555 50.594 1112 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.76 % Allowed : 13.81 % Favored : 83.43 % 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: 2.50 (0.26), residues: 979 helix: 1.85 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 1.18 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 117 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE D 204 TRP 0.008 0.001 TRP C 270 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8293) covalent geometry : angle 0.48409 / 0.25 (11226) hydrogen bonds : bond 0.04224 / 2.82 ( 586) hydrogen bonds : angle 3.91747 / 2.84 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6947 (tpt-90) cc_final: 0.6617 (mpt180) REVERT: A 89 ARG cc_start: 0.6040 (tmm160) cc_final: 0.5540 (ppt170) REVERT: A 101 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6152 (mp) REVERT: A 105 SER cc_start: 0.7106 (m) cc_final: 0.6894 (m) REVERT: A 210 ARG cc_start: 0.6169 (mtp-110) cc_final: 0.4777 (tmt170) REVERT: A 214 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6576 (ttm110) REVERT: A 236 TRP cc_start: 0.7394 (m-10) cc_final: 0.7093 (m100) REVERT: C 142 PHE cc_start: 0.7420 (m-10) cc_final: 0.7119 (m-10) REVERT: D 243 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6659 (ptp-170) REVERT: D 283 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 284 LYS cc_start: 0.7548 (pttt) cc_final: 0.6574 (tptp) REVERT: D 296 MET cc_start: 0.5863 (mpp) cc_final: 0.5206 (mtp) REVERT: D 298 GLU cc_start: 0.6925 (tp30) cc_final: 0.6433 (tp30) REVERT: D 301 GLU cc_start: 0.7918 (pt0) cc_final: 0.7459 (pt0) REVERT: D 328 GLU cc_start: 0.7980 (mp0) cc_final: 0.7678 (mp0) REVERT: B 231 PHE cc_start: 0.6039 (t80) cc_final: 0.5569 (m-80) REVERT: B 233 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5614 (mp10) REVERT: B 284 LYS cc_start: 0.7503 (pttt) cc_final: 0.7168 (pttp) REVERT: B 296 MET cc_start: 0.4206 (mpp) cc_final: 0.3252 (tpt) outliers start: 23 outliers final: 5 residues processed: 139 average time/residue: 0.5251 time to fit residues: 77.1551 Evaluate side-chains 124 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 330 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.204452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115000 restraints weight = 8843.299| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.44 r_work: 0.3130 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8293 Z= 0.131 Angle : 0.490 8.952 11226 Z= 0.256 Chirality : 0.037 0.156 1263 Planarity : 0.004 0.030 1348 Dihedral : 4.588 47.752 1112 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.76 % Allowed : 15.49 % Favored : 81.75 % 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: 2.59 (0.26), residues: 979 helix: 1.93 (0.18), residues: 777 sheet: None (None), residues: 0 loop : 1.12 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 153 TYR 0.010 0.001 TYR A 118 PHE 0.014 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8293) covalent geometry : angle 0.49027 / 0.26 (11226) hydrogen bonds : bond 0.04056 / 2.70 ( 586) hydrogen bonds : angle 3.86285 / 2.80 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6843 (tpt-90) cc_final: 0.6553 (mpt180) REVERT: A 89 ARG cc_start: 0.5954 (tmm160) cc_final: 0.5429 (ppt170) REVERT: A 105 SER cc_start: 0.7156 (m) cc_final: 0.6953 (m) REVERT: A 210 ARG cc_start: 0.6240 (mtp-110) cc_final: 0.4917 (tmt170) REVERT: A 214 ARG cc_start: 0.7357 (mtp85) cc_final: 0.6568 (ttm110) REVERT: A 236 TRP cc_start: 0.7387 (m-10) cc_final: 0.7100 (m100) REVERT: C 142 PHE cc_start: 0.7420 (m-10) cc_final: 0.7092 (m-10) REVERT: D 143 THR cc_start: 0.8171 (t) cc_final: 0.7840 (p) REVERT: D 243 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6830 (ptp-170) REVERT: D 284 LYS cc_start: 0.7574 (pttt) cc_final: 0.6618 (tptp) REVERT: D 296 MET cc_start: 0.5892 (mpp) cc_final: 0.5436 (mpp) REVERT: D 298 GLU cc_start: 0.6929 (tp30) cc_final: 0.6648 (tp30) REVERT: D 301 GLU cc_start: 0.7959 (pt0) cc_final: 0.7695 (pt0) REVERT: B 231 PHE cc_start: 0.6254 (t80) cc_final: 0.5684 (m-80) REVERT: B 284 LYS cc_start: 0.7482 (pttt) cc_final: 0.7203 (pttp) REVERT: B 296 MET cc_start: 0.4289 (mpp) cc_final: 0.3265 (tpt) outliers start: 23 outliers final: 11 residues processed: 136 average time/residue: 0.5180 time to fit residues: 74.4398 Evaluate side-chains 121 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 339 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.202862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112934 restraints weight = 8815.983| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.44 r_work: 0.3149 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8293 Z= 0.156 Angle : 0.500 8.841 11226 Z= 0.260 Chirality : 0.038 0.171 1263 Planarity : 0.004 0.031 1348 Dihedral : 4.836 57.053 1112 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.64 % Allowed : 16.33 % Favored : 81.03 % 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: 2.75 (0.26), residues: 979 helix: 2.00 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 1.39 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 236 TYR 0.010 0.001 TYR B 266 PHE 0.019 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8293) covalent geometry : angle 0.49970 / 0.26 (11226) hydrogen bonds : bond 0.04149 / 2.74 ( 586) hydrogen bonds : angle 3.85366 / 2.80 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6856 (tpt-90) cc_final: 0.6589 (mpt180) REVERT: A 89 ARG cc_start: 0.6055 (tmm160) cc_final: 0.5486 (ppt170) REVERT: A 210 ARG cc_start: 0.6313 (mtp-110) cc_final: 0.4933 (tmt170) REVERT: A 214 ARG cc_start: 0.7421 (mtp85) cc_final: 0.6549 (ttm110) REVERT: A 236 TRP cc_start: 0.7543 (m-10) cc_final: 0.7205 (m100) REVERT: D 117 ARG cc_start: 0.6194 (pmm150) cc_final: 0.5926 (pmt-80) REVERT: D 284 LYS cc_start: 0.7608 (pttt) cc_final: 0.6626 (tptp) REVERT: D 298 GLU cc_start: 0.6855 (tp30) cc_final: 0.6574 (tp30) REVERT: D 301 GLU cc_start: 0.8228 (pt0) cc_final: 0.7958 (pt0) REVERT: B 231 PHE cc_start: 0.6230 (t80) cc_final: 0.5516 (m-80) REVERT: B 284 LYS cc_start: 0.7543 (pttt) cc_final: 0.7290 (pttp) REVERT: B 296 MET cc_start: 0.4381 (mpp) cc_final: 0.3328 (tpt) REVERT: B 328 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6901 (mp0) REVERT: B 335 THR cc_start: 0.8988 (t) cc_final: 0.8617 (p) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.5487 time to fit residues: 73.4809 Evaluate side-chains 116 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.203446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114559 restraints weight = 8695.210| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.42 r_work: 0.3122 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8293 Z= 0.126 Angle : 0.488 11.253 11226 Z= 0.249 Chirality : 0.036 0.147 1263 Planarity : 0.003 0.030 1348 Dihedral : 4.816 58.191 1112 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.92 % Allowed : 17.89 % Favored : 80.19 % 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: 2.87 (0.26), residues: 979 helix: 2.10 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 1.35 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.009 0.001 TYR B 266 PHE 0.017 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8293) covalent geometry : angle 0.48833 / 0.25 (11226) hydrogen bonds : bond 0.03825 / 2.55 ( 586) hydrogen bonds : angle 3.74256 / 2.72 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6904 (tpt-90) cc_final: 0.6583 (mpt180) REVERT: A 89 ARG cc_start: 0.5954 (tmm160) cc_final: 0.5400 (ppt170) REVERT: A 101 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6248 (mp) REVERT: A 210 ARG cc_start: 0.6238 (mtp-110) cc_final: 0.4890 (tmt170) REVERT: A 214 ARG cc_start: 0.7412 (mtp85) cc_final: 0.6517 (ttm110) REVERT: A 236 TRP cc_start: 0.7579 (m-10) cc_final: 0.7216 (m100) REVERT: A 242 CYS cc_start: 0.8530 (t) cc_final: 0.7925 (m) REVERT: D 284 LYS cc_start: 0.7602 (pttt) cc_final: 0.6597 (tptt) REVERT: D 296 MET cc_start: 0.6072 (mpp) cc_final: 0.5311 (mtp) REVERT: D 298 GLU cc_start: 0.6828 (tp30) cc_final: 0.6603 (tp30) REVERT: D 301 GLU cc_start: 0.8225 (pt0) cc_final: 0.8001 (pt0) REVERT: B 231 PHE cc_start: 0.6507 (t80) cc_final: 0.5859 (m-80) REVERT: B 284 LYS cc_start: 0.7467 (pttt) cc_final: 0.7218 (pttp) REVERT: B 296 MET cc_start: 0.4294 (mpp) cc_final: 0.3269 (tpt) REVERT: B 327 TRP cc_start: 0.6872 (p-90) cc_final: 0.6585 (p-90) outliers start: 16 outliers final: 11 residues processed: 124 average time/residue: 0.5418 time to fit residues: 70.9544 Evaluate side-chains 116 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 339 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.203297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114341 restraints weight = 8782.640| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.42 r_work: 0.3119 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8293 Z= 0.129 Angle : 0.502 11.721 11226 Z= 0.256 Chirality : 0.037 0.137 1263 Planarity : 0.004 0.038 1348 Dihedral : 4.812 59.186 1112 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.16 % Allowed : 18.37 % Favored : 79.47 % 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: 2.99 (0.26), residues: 979 helix: 2.19 (0.18), residues: 773 sheet: None (None), residues: 0 loop : 1.39 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.009 0.001 TYR B 266 PHE 0.025 0.001 PHE D 130 TRP 0.008 0.001 TRP C 270 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8293) covalent geometry : angle 0.50194 / 0.26 (11226) hydrogen bonds : bond 0.03769 / 2.50 ( 586) hydrogen bonds : angle 3.73824 / 2.72 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6947 (tpt-90) cc_final: 0.6620 (mpt180) REVERT: A 89 ARG cc_start: 0.5728 (tmm160) cc_final: 0.5251 (ppt170) REVERT: A 210 ARG cc_start: 0.6294 (mtp-110) cc_final: 0.4942 (tmt170) REVERT: A 214 ARG cc_start: 0.7422 (mtp85) cc_final: 0.6520 (ttm110) REVERT: A 236 TRP cc_start: 0.7584 (m-10) cc_final: 0.7217 (m100) REVERT: A 242 CYS cc_start: 0.8559 (t) cc_final: 0.7949 (m) REVERT: D 284 LYS cc_start: 0.7526 (pttt) cc_final: 0.6497 (tptt) REVERT: D 296 MET cc_start: 0.6008 (mpp) cc_final: 0.5231 (mtp) REVERT: D 298 GLU cc_start: 0.6873 (tp30) cc_final: 0.6621 (tp30) REVERT: B 231 PHE cc_start: 0.6496 (t80) cc_final: 0.5792 (m-80) REVERT: B 284 LYS cc_start: 0.7467 (pttt) cc_final: 0.6456 (tptt) REVERT: B 296 MET cc_start: 0.4295 (mpp) cc_final: 0.3295 (tpt) REVERT: B 327 TRP cc_start: 0.6986 (p-90) cc_final: 0.6677 (p-90) REVERT: B 335 THR cc_start: 0.8999 (t) cc_final: 0.8644 (p) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.5192 time to fit residues: 64.7908 Evaluate side-chains 114 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 361 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.203720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116009 restraints weight = 8679.657| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.38 r_work: 0.3140 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8293 Z= 0.117 Angle : 0.491 12.441 11226 Z= 0.248 Chirality : 0.036 0.150 1263 Planarity : 0.003 0.035 1348 Dihedral : 4.774 59.381 1112 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.92 % Allowed : 18.73 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.01 (0.26), residues: 979 helix: 2.21 (0.18), residues: 778 sheet: None (None), residues: 0 loop : 1.32 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.022 0.001 TYR C 154 PHE 0.021 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8293) covalent geometry : angle 0.49054 / 0.25 (11226) hydrogen bonds : bond 0.03634 / 2.42 ( 586) hydrogen bonds : angle 3.68081 / 2.68 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6885 (tpt-90) cc_final: 0.6604 (mpt180) REVERT: A 89 ARG cc_start: 0.5651 (tmm160) cc_final: 0.5172 (ppt170) REVERT: A 153 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7180 (mtm110) REVERT: A 210 ARG cc_start: 0.6264 (mtp-110) cc_final: 0.4912 (tmt170) REVERT: A 214 ARG cc_start: 0.7329 (mtp85) cc_final: 0.6462 (ttm110) REVERT: A 236 TRP cc_start: 0.7443 (m-10) cc_final: 0.7085 (m100) REVERT: A 242 CYS cc_start: 0.8389 (t) cc_final: 0.7753 (m) REVERT: D 143 THR cc_start: 0.7970 (t) cc_final: 0.7565 (p) REVERT: D 284 LYS cc_start: 0.7372 (pttt) cc_final: 0.6287 (tptt) REVERT: D 296 MET cc_start: 0.6069 (mpp) cc_final: 0.5229 (mtp) REVERT: D 298 GLU cc_start: 0.6736 (tp30) cc_final: 0.6483 (tp30) REVERT: B 231 PHE cc_start: 0.6466 (t80) cc_final: 0.5721 (m-80) REVERT: B 284 LYS cc_start: 0.7310 (pttt) cc_final: 0.6363 (tptt) REVERT: B 296 MET cc_start: 0.4257 (mpp) cc_final: 0.3294 (tpt) REVERT: B 327 TRP cc_start: 0.6869 (p-90) cc_final: 0.6516 (p-90) REVERT: B 335 THR cc_start: 0.8873 (t) cc_final: 0.8516 (p) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.5934 time to fit residues: 75.0978 Evaluate side-chains 117 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 361 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.203566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114553 restraints weight = 8732.013| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.42 r_work: 0.3180 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8293 Z= 0.127 Angle : 0.506 12.280 11226 Z= 0.255 Chirality : 0.036 0.166 1263 Planarity : 0.004 0.046 1348 Dihedral : 4.748 58.835 1112 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.28 % Allowed : 18.61 % Favored : 79.11 % 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: 3.20 (0.26), residues: 979 helix: 2.35 (0.18), residues: 769 sheet: None (None), residues: 0 loop : 1.40 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 153 TYR 0.012 0.001 TYR C 154 PHE 0.021 0.001 PHE D 130 TRP 0.009 0.001 TRP D 327 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8293) covalent geometry : angle 0.50639 / 0.26 (11226) hydrogen bonds : bond 0.03678 / 2.45 ( 586) hydrogen bonds : angle 3.67745 / 2.68 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6993 (tpt-90) cc_final: 0.6752 (mpt180) REVERT: A 89 ARG cc_start: 0.5613 (tmm160) cc_final: 0.5097 (ppt170) REVERT: A 153 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7185 (mtm110) REVERT: A 210 ARG cc_start: 0.6328 (mtp-110) cc_final: 0.4952 (tpt170) REVERT: A 214 ARG cc_start: 0.7394 (mtp85) cc_final: 0.6496 (ttm110) REVERT: A 236 TRP cc_start: 0.7629 (m-10) cc_final: 0.7206 (m100) REVERT: A 242 CYS cc_start: 0.8529 (t) cc_final: 0.7919 (m) REVERT: C 328 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5524 (m-70) REVERT: D 284 LYS cc_start: 0.7426 (pttt) cc_final: 0.6357 (tptt) REVERT: D 296 MET cc_start: 0.6046 (mpp) cc_final: 0.5239 (mtp) REVERT: D 298 GLU cc_start: 0.6827 (tp30) cc_final: 0.6556 (tp30) REVERT: B 284 LYS cc_start: 0.7388 (pttt) cc_final: 0.6418 (tptt) REVERT: B 296 MET cc_start: 0.4278 (mpp) cc_final: 0.3332 (tpt) REVERT: B 327 TRP cc_start: 0.7020 (p-90) cc_final: 0.6665 (p-90) REVERT: B 335 THR cc_start: 0.8979 (t) cc_final: 0.8614 (p) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.5334 time to fit residues: 68.2799 Evaluate side-chains 116 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 361 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.203816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114740 restraints weight = 8722.861| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.42 r_work: 0.3126 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8293 Z= 0.128 Angle : 0.509 13.387 11226 Z= 0.256 Chirality : 0.036 0.171 1263 Planarity : 0.004 0.058 1348 Dihedral : 4.774 58.231 1112 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.16 % Allowed : 19.33 % Favored : 78.51 % 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: 3.18 (0.26), residues: 979 helix: 2.35 (0.18), residues: 769 sheet: None (None), residues: 0 loop : 1.35 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 153 TYR 0.014 0.001 TYR C 154 PHE 0.022 0.001 PHE D 130 TRP 0.008 0.001 TRP C 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8293) covalent geometry : angle 0.50880 / 0.26 (11226) hydrogen bonds : bond 0.03665 / 2.44 ( 586) hydrogen bonds : angle 3.66439 / 2.68 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6953 (tpt-90) cc_final: 0.6746 (mpt180) REVERT: A 89 ARG cc_start: 0.5627 (tmm160) cc_final: 0.5105 (ppt170) REVERT: A 153 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7216 (mtm110) REVERT: A 210 ARG cc_start: 0.6291 (mtp-110) cc_final: 0.4798 (tpt170) REVERT: A 214 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6422 (ttm110) REVERT: A 236 TRP cc_start: 0.7648 (m-10) cc_final: 0.7234 (m100) REVERT: A 242 CYS cc_start: 0.8525 (t) cc_final: 0.7921 (m) REVERT: C 117 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: C 231 GLU cc_start: 0.8253 (mp0) cc_final: 0.7986 (mp0) REVERT: D 238 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7635 (tt) REVERT: D 249 LEU cc_start: 0.8252 (tp) cc_final: 0.8001 (tt) REVERT: D 284 LYS cc_start: 0.7401 (pttt) cc_final: 0.6343 (tptt) REVERT: D 296 MET cc_start: 0.6019 (mpp) cc_final: 0.5213 (mtp) REVERT: D 298 GLU cc_start: 0.6776 (tp30) cc_final: 0.6540 (tp30) REVERT: B 284 LYS cc_start: 0.7401 (pttt) cc_final: 0.6409 (tptt) REVERT: B 296 MET cc_start: 0.4337 (mpp) cc_final: 0.3349 (tpt) REVERT: B 335 THR cc_start: 0.8969 (t) cc_final: 0.8607 (p) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.5384 time to fit residues: 65.2919 Evaluate side-chains 118 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 361 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.203651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114918 restraints weight = 8698.334| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.39 r_work: 0.3183 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8293 Z= 0.127 Angle : 0.519 13.522 11226 Z= 0.260 Chirality : 0.037 0.171 1263 Planarity : 0.004 0.055 1348 Dihedral : 4.777 57.249 1112 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.92 % Allowed : 19.45 % Favored : 78.63 % 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: 3.23 (0.26), residues: 979 helix: 2.38 (0.18), residues: 769 sheet: None (None), residues: 0 loop : 1.39 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 153 TYR 0.010 0.001 TYR C 154 PHE 0.021 0.001 PHE D 130 TRP 0.008 0.001 TRP C 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8293) covalent geometry : angle 0.51922 / 0.26 (11226) hydrogen bonds : bond 0.03660 / 2.44 ( 586) hydrogen bonds : angle 3.65018 / 2.67 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.64 seconds wall clock time: 61 minutes 11.46 seconds (3671.46 seconds total)