Starting phenix.real_space_refine on Thu Jul 2 10:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22bk_68153/07_2026/22bk_68153.cif Found real_map, /net/cci-nas-00/data/ceres_data/22bk_68153/07_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_68153/07_2026/22bk_68153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22bk_68153/07_2026/22bk_68153.map" model { file = "/net/cci-nas-00/data/ceres_data/22bk_68153/07_2026/22bk_68153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22bk_68153/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 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: 0.69 Conformation dependent library (CDL) restraints added in 429.1 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: 0.21 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: 1.30 Time building geometry restraints manager: 0.92 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: 1.610 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.160 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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 : 0.330 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: 0.6679 time to fit residues: 133.9010 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 : 0.296 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.203030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116199 restraints weight = 8818.619| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.39 r_work: 0.3208 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8293 Z= 0.180 Angle : 0.568 9.416 11226 Z= 0.300 Chirality : 0.041 0.175 1263 Planarity : 0.006 0.081 1348 Dihedral : 4.759 53.535 1112 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 2.13 (0.26), residues: 979 helix: 1.51 (0.18), residues: 765 sheet: None (None), residues: 0 loop : 1.42 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 190 TYR 0.012 0.002 TYR A 74 PHE 0.017 0.002 PHE D 204 TRP 0.013 0.001 TRP B 187 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8293) covalent geometry : angle 0.56843 / 0.30 (11226) hydrogen bonds : bond 0.04820 / 3.17 ( 586) hydrogen bonds : angle 4.26243 / 3.10 ( 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 160 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6137 (tmm160) cc_final: 0.5572 (ppt170) REVERT: A 101 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6306 (mp) REVERT: A 210 ARG cc_start: 0.5884 (mtp-110) cc_final: 0.5611 (ptm-80) REVERT: A 214 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6648 (ttm110) REVERT: A 236 TRP cc_start: 0.7560 (m-10) cc_final: 0.7132 (m100) REVERT: C 78 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6866 (mm-40) REVERT: C 142 PHE cc_start: 0.7549 (m-10) cc_final: 0.7239 (m-10) REVERT: C 214 ARG cc_start: 0.7438 (mpt180) cc_final: 0.6454 (mtp85) REVERT: C 242 CYS cc_start: 0.8682 (t) cc_final: 0.8290 (m) REVERT: D 117 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6393 (pmm150) REVERT: D 243 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6678 (ptp-170) REVERT: D 284 LYS cc_start: 0.7453 (pttt) cc_final: 0.6493 (tptp) REVERT: D 296 MET cc_start: 0.5780 (mpp) cc_final: 0.5424 (mpt) REVERT: D 298 GLU cc_start: 0.6983 (tp30) cc_final: 0.6567 (tp30) REVERT: D 301 GLU cc_start: 0.8018 (pt0) cc_final: 0.7528 (pt0) REVERT: B 231 PHE cc_start: 0.5862 (t80) cc_final: 0.5457 (m-80) REVERT: B 233 GLN cc_start: 0.5824 (OUTLIER) cc_final: 0.5605 (mp10) REVERT: B 237 MET cc_start: 0.8435 (mmm) cc_final: 0.8188 (mmm) REVERT: B 248 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7399 (mttt) REVERT: B 262 ILE cc_start: 0.8911 (mt) cc_final: 0.8711 (mm) REVERT: B 284 LYS cc_start: 0.7550 (pttt) cc_final: 0.7256 (pttp) REVERT: B 296 MET cc_start: 0.4389 (mpp) cc_final: 0.3275 (tpt) outliers start: 26 outliers final: 9 residues processed: 151 average time/residue: 0.6574 time to fit residues: 104.5617 Evaluate side-chains 129 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 C residue 328 HIS Chi-restraints excluded: chain D residue 117 ARG 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 B residue 190 ARG Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 248 LYS 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: 0.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.204240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116673 restraints weight = 8681.122| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.40 r_work: 0.3218 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8293 Z= 0.136 Angle : 0.505 8.968 11226 Z= 0.263 Chirality : 0.038 0.171 1263 Planarity : 0.004 0.041 1348 Dihedral : 4.693 50.268 1112 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.88 % Allowed : 14.65 % Favored : 82.47 % 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: 2.48 (0.26), residues: 979 helix: 1.83 (0.18), residues: 767 sheet: None (None), residues: 0 loop : 1.21 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 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 0.00305 / 0.14 ( 8293) covalent geometry : angle 0.50539 / 0.26 (11226) hydrogen bonds : bond 0.04310 / 2.87 ( 586) hydrogen bonds : angle 3.98297 / 2.89 ( 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 150 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6933 (tpt-90) cc_final: 0.6587 (mpt180) REVERT: A 89 ARG cc_start: 0.6070 (tmm160) cc_final: 0.5548 (ppt170) REVERT: A 101 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6239 (mp) REVERT: A 210 ARG cc_start: 0.6074 (mtp-110) cc_final: 0.4701 (tmt170) REVERT: A 214 ARG cc_start: 0.7393 (mtp85) cc_final: 0.6573 (ttm110) REVERT: A 236 TRP cc_start: 0.7399 (m-10) cc_final: 0.7039 (m100) REVERT: C 75 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7480 (tpp-160) REVERT: C 142 PHE cc_start: 0.7463 (m-10) cc_final: 0.7163 (m-10) REVERT: C 153 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6768 (ttp-110) REVERT: C 214 ARG cc_start: 0.7382 (mpt180) cc_final: 0.6400 (mtp85) REVERT: D 117 ARG cc_start: 0.6944 (pmt170) cc_final: 0.6632 (pmm150) REVERT: D 143 THR cc_start: 0.8053 (t) cc_final: 0.7733 (p) REVERT: D 243 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6650 (ptp-170) REVERT: D 284 LYS cc_start: 0.7375 (pttt) cc_final: 0.6405 (tptp) REVERT: D 296 MET cc_start: 0.5907 (mpp) cc_final: 0.5207 (mtp) REVERT: D 298 GLU cc_start: 0.6925 (tp30) cc_final: 0.6580 (tp30) REVERT: D 301 GLU cc_start: 0.8037 (pt0) cc_final: 0.7715 (pt0) REVERT: D 358 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7254 (tppt) REVERT: B 231 PHE cc_start: 0.5871 (t80) cc_final: 0.5476 (m-80) REVERT: B 233 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5593 (mp10) REVERT: B 248 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7390 (mttt) REVERT: B 284 LYS cc_start: 0.7454 (pttt) cc_final: 0.7132 (pttp) REVERT: B 296 MET cc_start: 0.4318 (mpp) cc_final: 0.3306 (tpt) outliers start: 24 outliers final: 6 residues processed: 140 average time/residue: 0.6593 time to fit residues: 97.1569 Evaluate side-chains 127 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 D residue 361 GLU Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 248 LYS 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: 0.6980 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.202880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114456 restraints weight = 8934.438| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.44 r_work: 0.3185 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8293 Z= 0.150 Angle : 0.505 8.852 11226 Z= 0.262 Chirality : 0.037 0.143 1263 Planarity : 0.004 0.031 1348 Dihedral : 4.801 56.074 1112 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.88 % Allowed : 15.73 % Favored : 81.39 % 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: 2.65 (0.26), residues: 979 helix: 1.96 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 1.26 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 117 TYR 0.021 0.001 TYR C 74 PHE 0.016 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8293) covalent geometry : angle 0.50538 / 0.26 (11226) hydrogen bonds : bond 0.04102 / 2.71 ( 586) hydrogen bonds : angle 3.88698 / 2.82 ( 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: 24 poor density : 118 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6816 (tpt-90) cc_final: 0.6522 (mpt180) REVERT: A 89 ARG cc_start: 0.6004 (tmm160) cc_final: 0.5434 (ppt170) REVERT: A 210 ARG cc_start: 0.6265 (mtp-110) cc_final: 0.4920 (tmt170) REVERT: A 214 ARG cc_start: 0.7391 (mtp85) cc_final: 0.6518 (ttm110) REVERT: A 236 TRP cc_start: 0.7482 (m-10) cc_final: 0.7105 (m100) REVERT: C 142 PHE cc_start: 0.7546 (m-10) cc_final: 0.7316 (m-10) REVERT: C 153 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6965 (ttp-110) REVERT: D 143 THR cc_start: 0.8102 (t) cc_final: 0.7720 (p) REVERT: D 243 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6659 (ptp-170) REVERT: D 284 LYS cc_start: 0.7479 (pttt) cc_final: 0.6487 (tptp) REVERT: D 298 GLU cc_start: 0.6776 (tp30) cc_final: 0.6495 (tp30) REVERT: D 301 GLU cc_start: 0.8155 (pt0) cc_final: 0.7899 (pt0) REVERT: B 231 PHE cc_start: 0.6089 (t80) cc_final: 0.5485 (m-80) REVERT: B 248 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7434 (mttt) REVERT: B 284 LYS cc_start: 0.7471 (pttt) cc_final: 0.7190 (pttp) REVERT: B 296 MET cc_start: 0.4394 (mpp) cc_final: 0.3325 (tpt) REVERT: B 335 THR cc_start: 0.8926 (t) cc_final: 0.8531 (p) outliers start: 24 outliers final: 12 residues processed: 135 average time/residue: 0.6239 time to fit residues: 88.8123 Evaluate side-chains 120 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 203 LEU 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 243 ARG Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 248 LYS 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: 2.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.201624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113097 restraints weight = 8877.540| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.42 r_work: 0.3166 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8293 Z= 0.169 Angle : 0.512 8.927 11226 Z= 0.265 Chirality : 0.038 0.144 1263 Planarity : 0.003 0.031 1348 Dihedral : 4.927 58.600 1112 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.24 % Allowed : 16.57 % 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: 2.68 (0.26), residues: 979 helix: 1.97 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 1.28 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.018 0.001 TYR C 74 PHE 0.021 0.001 PHE D 130 TRP 0.010 0.001 TRP C 270 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8293) covalent geometry : angle 0.51159 / 0.26 (11226) hydrogen bonds : bond 0.04173 / 2.75 ( 586) hydrogen bonds : angle 3.91383 / 2.84 ( 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 142 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6522 (mpt180) REVERT: A 89 ARG cc_start: 0.5966 (tmm160) cc_final: 0.5438 (ppt170) REVERT: A 101 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6176 (mp) REVERT: A 210 ARG cc_start: 0.6234 (mtp-110) cc_final: 0.4893 (tmt170) REVERT: A 214 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6487 (ttm110) REVERT: A 236 TRP cc_start: 0.7475 (m-10) cc_final: 0.7102 (m100) REVERT: A 242 CYS cc_start: 0.8468 (t) cc_final: 0.7897 (m) REVERT: C 153 ARG cc_start: 0.7317 (mtp85) cc_final: 0.7070 (ttp-110) REVERT: D 143 THR cc_start: 0.8051 (t) cc_final: 0.7655 (p) REVERT: D 155 TRP cc_start: 0.6411 (OUTLIER) cc_final: 0.5658 (m-10) REVERT: D 284 LYS cc_start: 0.7497 (pttt) cc_final: 0.6527 (tptt) REVERT: D 296 MET cc_start: 0.5978 (mpp) cc_final: 0.5159 (mtp) REVERT: D 298 GLU cc_start: 0.6781 (tp30) cc_final: 0.6559 (tp30) REVERT: B 231 PHE cc_start: 0.6227 (t80) cc_final: 0.5564 (m-80) REVERT: B 248 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7435 (mttt) REVERT: B 284 LYS cc_start: 0.7553 (pttt) cc_final: 0.7288 (pttp) REVERT: B 296 MET cc_start: 0.4405 (mpp) cc_final: 0.3350 (tpt) REVERT: B 328 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6824 (pm20) REVERT: B 335 THR cc_start: 0.8918 (t) cc_final: 0.8501 (p) outliers start: 27 outliers final: 10 residues processed: 134 average time/residue: 0.5724 time to fit residues: 80.7575 Evaluate side-chains 121 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU 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 134 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 155 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 339 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.205983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119983 restraints weight = 8802.201| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.42 r_work: 0.3261 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8293 Z= 0.102 Angle : 0.477 10.572 11226 Z= 0.244 Chirality : 0.035 0.150 1263 Planarity : 0.003 0.037 1348 Dihedral : 4.804 58.562 1112 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.28 % Allowed : 17.77 % Favored : 79.95 % 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: 2.91 (0.26), residues: 979 helix: 2.17 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 1.17 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.010 0.001 TYR A 82 PHE 0.021 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 8293) covalent geometry : angle 0.47700 / 0.24 (11226) hydrogen bonds : bond 0.03503 / 2.34 ( 586) hydrogen bonds : angle 3.68583 / 2.68 ( 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 138 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6918 (tpt-90) cc_final: 0.6696 (mpt180) REVERT: A 89 ARG cc_start: 0.5853 (tmm160) cc_final: 0.5347 (ppt170) REVERT: A 210 ARG cc_start: 0.6200 (mtp-110) cc_final: 0.4865 (tmt170) REVERT: A 214 ARG cc_start: 0.7369 (mtp85) cc_final: 0.6469 (ttm110) REVERT: A 236 TRP cc_start: 0.7404 (m-10) cc_final: 0.7054 (m100) REVERT: C 153 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7083 (ttp-110) REVERT: D 143 THR cc_start: 0.8052 (t) cc_final: 0.7697 (p) REVERT: D 243 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6566 (ptp-170) REVERT: D 284 LYS cc_start: 0.7389 (pttt) cc_final: 0.6346 (tptt) REVERT: D 296 MET cc_start: 0.6085 (mpp) cc_final: 0.5212 (mtp) REVERT: D 298 GLU cc_start: 0.6784 (tp30) cc_final: 0.6535 (tp30) REVERT: D 358 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7219 (tppt) REVERT: B 231 PHE cc_start: 0.6229 (t80) cc_final: 0.5497 (m-80) REVERT: B 284 LYS cc_start: 0.7375 (pttt) cc_final: 0.6442 (tptt) REVERT: B 296 MET cc_start: 0.4263 (mpp) cc_final: 0.3265 (tpt) REVERT: B 327 TRP cc_start: 0.6788 (p-90) cc_final: 0.6477 (p-90) REVERT: B 358 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7512 (tptt) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 0.5316 time to fit residues: 72.9729 Evaluate side-chains 119 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE 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 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 Chi-restraints excluded: chain B residue 361 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.202729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114602 restraints weight = 8865.401| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.40 r_work: 0.3187 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8293 Z= 0.148 Angle : 0.519 10.873 11226 Z= 0.262 Chirality : 0.037 0.167 1263 Planarity : 0.004 0.030 1348 Dihedral : 4.822 57.533 1112 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.88 % Allowed : 17.29 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.89 (0.26), residues: 979 helix: 2.20 (0.18), residues: 777 sheet: None (None), residues: 0 loop : 0.91 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.021 0.001 TYR C 74 PHE 0.023 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8293) covalent geometry : angle 0.51890 / 0.26 (11226) hydrogen bonds : bond 0.03876 / 2.56 ( 586) hydrogen bonds : angle 3.74549 / 2.73 ( 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 133 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6932 (tpt-90) cc_final: 0.6635 (mpt180) REVERT: A 89 ARG cc_start: 0.5704 (tmm160) cc_final: 0.5221 (ppt170) REVERT: A 153 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7192 (mtm110) REVERT: A 210 ARG cc_start: 0.6303 (mtp-110) cc_final: 0.4948 (tmt170) REVERT: A 214 ARG cc_start: 0.7426 (mtp85) cc_final: 0.6502 (ttm110) REVERT: A 236 TRP cc_start: 0.7510 (m-10) cc_final: 0.7135 (m100) REVERT: C 153 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7150 (ttp-110) REVERT: C 231 GLU cc_start: 0.8225 (mp0) cc_final: 0.7959 (mp0) REVERT: D 143 THR cc_start: 0.8031 (t) cc_final: 0.7650 (p) REVERT: D 243 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6659 (ptp-170) REVERT: D 284 LYS cc_start: 0.7482 (pttt) cc_final: 0.6436 (tptt) REVERT: D 296 MET cc_start: 0.6134 (mpp) cc_final: 0.5251 (mtp) REVERT: B 284 LYS cc_start: 0.7452 (pttt) cc_final: 0.7211 (pttp) REVERT: B 296 MET cc_start: 0.4304 (mpp) cc_final: 0.3314 (tpt) REVERT: B 327 TRP cc_start: 0.6950 (p-90) cc_final: 0.6505 (p-90) REVERT: B 328 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6818 (mp0) REVERT: B 335 THR cc_start: 0.8911 (t) cc_final: 0.8546 (p) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 0.5044 time to fit residues: 66.1224 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 : 0.202 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 142 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 361 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.203790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116580 restraints weight = 8795.457| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.40 r_work: 0.3215 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4410 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= 0.122 Angle : 0.494 11.621 11226 Z= 0.250 Chirality : 0.036 0.144 1263 Planarity : 0.003 0.030 1348 Dihedral : 4.768 57.398 1112 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.16 % Allowed : 18.73 % 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: 3.13 (0.26), residues: 979 helix: 2.33 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 1.25 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.021 0.001 TYR C 74 PHE 0.024 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 0.00281 / 0.12 ( 8293) covalent geometry : angle 0.49406 / 0.25 (11226) hydrogen bonds : bond 0.03647 / 2.42 ( 586) hydrogen bonds : angle 3.68940 / 2.69 ( 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 122 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6981 (tpt-90) cc_final: 0.6738 (mpt180) REVERT: A 89 ARG cc_start: 0.5615 (tmm160) cc_final: 0.5099 (ppt170) REVERT: A 210 ARG cc_start: 0.6282 (mtp-110) cc_final: 0.4964 (tmt170) REVERT: A 214 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6418 (ttm110) REVERT: A 236 TRP cc_start: 0.7490 (m-10) cc_final: 0.7128 (m100) REVERT: C 153 ARG cc_start: 0.7423 (mtp85) cc_final: 0.7197 (ttp-110) REVERT: D 143 THR cc_start: 0.8015 (t) cc_final: 0.7633 (p) REVERT: D 284 LYS cc_start: 0.7406 (pttt) cc_final: 0.6372 (tptt) REVERT: D 296 MET cc_start: 0.6142 (mpp) cc_final: 0.5254 (mtp) REVERT: D 358 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7208 (tppt) REVERT: B 284 LYS cc_start: 0.7361 (pttt) cc_final: 0.6413 (tptt) REVERT: B 296 MET cc_start: 0.4282 (mpp) cc_final: 0.3324 (tpt) REVERT: B 327 TRP cc_start: 0.6921 (p-90) cc_final: 0.6589 (p-90) REVERT: B 335 THR cc_start: 0.8895 (t) cc_final: 0.8547 (p) outliers start: 18 outliers final: 10 residues processed: 117 average time/residue: 0.4810 time to fit residues: 59.5492 Evaluate side-chains 113 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR 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 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: 0.4980 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.201652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112541 restraints weight = 8781.646| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.41 r_work: 0.3162 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8293 Z= 0.167 Angle : 0.538 13.236 11226 Z= 0.270 Chirality : 0.038 0.172 1263 Planarity : 0.004 0.032 1348 Dihedral : 4.842 56.312 1112 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.52 % Allowed : 18.61 % Favored : 78.87 % 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: 3.05 (0.26), residues: 979 helix: 2.27 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 1.22 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.021 0.001 TYR C 74 PHE 0.020 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 8293) covalent geometry : angle 0.53796 / 0.27 (11226) hydrogen bonds : bond 0.03974 / 2.62 ( 586) hydrogen bonds : angle 3.80052 / 2.77 ( 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 130 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6868 (tpt-90) cc_final: 0.6653 (mpt180) REVERT: A 89 ARG cc_start: 0.5570 (tmm160) cc_final: 0.5068 (ppt170) REVERT: A 153 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7246 (mtm110) REVERT: A 210 ARG cc_start: 0.6394 (mtp-110) cc_final: 0.5071 (tmt170) REVERT: A 214 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6379 (ttm110) REVERT: A 236 TRP cc_start: 0.7521 (m-10) cc_final: 0.7153 (m100) REVERT: C 153 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7366 (ttp-110) REVERT: D 143 THR cc_start: 0.8001 (t) cc_final: 0.7616 (p) REVERT: D 243 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6793 (ptp-170) REVERT: D 249 LEU cc_start: 0.8297 (tp) cc_final: 0.8040 (tt) REVERT: D 284 LYS cc_start: 0.7422 (pttt) cc_final: 0.6378 (tptt) REVERT: D 296 MET cc_start: 0.6032 (mpp) cc_final: 0.5302 (mtp) REVERT: B 284 LYS cc_start: 0.7456 (pttt) cc_final: 0.7230 (pttp) REVERT: B 296 MET cc_start: 0.4380 (mpp) cc_final: 0.3373 (tpt) REVERT: B 327 TRP cc_start: 0.7017 (p-90) cc_final: 0.6694 (p-90) REVERT: B 328 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6719 (mp0) REVERT: B 335 THR cc_start: 0.8887 (t) cc_final: 0.8505 (p) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.6024 time to fit residues: 76.1325 Evaluate side-chains 120 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 298 THR 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 D residue 151 VAL 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 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: 0.7980 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.202796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116163 restraints weight = 8797.174| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.35 r_work: 0.3201 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4615 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= 0.130 Angle : 0.520 13.484 11226 Z= 0.259 Chirality : 0.036 0.150 1263 Planarity : 0.003 0.030 1348 Dihedral : 4.763 54.656 1112 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.04 % Allowed : 19.81 % Favored : 78.15 % 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: 3.12 (0.26), residues: 979 helix: 2.34 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 1.17 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.022 0.001 TYR C 74 PHE 0.018 0.001 PHE D 130 TRP 0.009 0.001 TRP C 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8293) covalent geometry : angle 0.52021 / 0.26 (11226) hydrogen bonds : bond 0.03704 / 2.46 ( 586) hydrogen bonds : angle 3.72080 / 2.72 ( 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 124 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.5604 (tmm160) cc_final: 0.5078 (ppt-90) REVERT: A 153 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7233 (mtm110) REVERT: A 210 ARG cc_start: 0.6375 (mtp-110) cc_final: 0.4953 (tmt170) REVERT: A 214 ARG cc_start: 0.7302 (mtp85) cc_final: 0.6383 (ttm110) REVERT: A 236 TRP cc_start: 0.7584 (m-10) cc_final: 0.7149 (m100) REVERT: C 117 GLU cc_start: 0.8504 (pt0) cc_final: 0.8192 (pm20) REVERT: D 143 THR cc_start: 0.7971 (t) cc_final: 0.7579 (p) REVERT: D 284 LYS cc_start: 0.7355 (pttt) cc_final: 0.6266 (tptt) REVERT: D 296 MET cc_start: 0.6116 (mpp) cc_final: 0.5358 (mtp) REVERT: B 284 LYS cc_start: 0.7380 (pttt) cc_final: 0.7155 (pttp) REVERT: B 296 MET cc_start: 0.4415 (mpp) cc_final: 0.3447 (tpt) REVERT: B 335 THR cc_start: 0.8897 (t) cc_final: 0.8527 (p) outliers start: 17 outliers final: 13 residues processed: 117 average time/residue: 0.5853 time to fit residues: 72.0987 Evaluate side-chains 114 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 298 THR 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 259 ASP Chi-restraints excluded: chain C residue 260 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 50 optimal weight: 0.0020 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 33 optimal weight: 0.0050 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.204870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117671 restraints weight = 8771.758| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.39 r_work: 0.3226 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4686 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= 0.113 Angle : 0.517 13.325 11226 Z= 0.257 Chirality : 0.036 0.147 1263 Planarity : 0.003 0.053 1348 Dihedral : 4.714 54.194 1112 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.04 % Allowed : 19.81 % Favored : 78.15 % 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: 3.21 (0.26), residues: 979 helix: 2.41 (0.18), residues: 767 sheet: None (None), residues: 0 loop : 1.22 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 153 TYR 0.022 0.001 TYR C 74 PHE 0.018 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 0.00257 / 0.11 ( 8293) covalent geometry : angle 0.51737 / 0.26 (11226) hydrogen bonds : bond 0.03511 / 2.34 ( 586) hydrogen bonds : angle 3.63363 / 2.66 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3883.02 seconds wall clock time: 66 minutes 38.39 seconds (3998.39 seconds total)