Starting phenix.real_space_refine on Tue Mar 3 18:23:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.map" model { file = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2026/6p9y_20278.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5099 2.51 5 N 1386 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7994 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1645 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2143 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.17 Number of scatterers: 7994 At special positions: 0 Unit cell: (80.948, 96.642, 142.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1460 8.00 N 1386 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.04 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: 0.72 Conformation dependent library (CDL) restraints added in 253.5 milliseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 40.7% alpha, 18.2% 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 13 through 40 removed outlier: 3.579A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.664A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.275A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.640A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.966A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 4.439A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.646A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.922A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.683A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.803A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.653A pdb=" N PHE P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP P 8 " --> pdb=" O GLY P 4 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 164 removed outlier: 3.622A pdb=" N LEU R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 178 removed outlier: 3.747A pdb=" N THR R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 211 removed outlier: 3.674A pdb=" N TRP R 208 " --> pdb=" O PHE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.980A pdb=" N VAL R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 274 removed outlier: 3.697A pdb=" N ILE R 271 " --> pdb=" O TYR R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 289 Processing helix chain 'R' and resid 302 through 337 removed outlier: 4.001A pdb=" N VAL R 308 " --> pdb=" O ALA R 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.583A pdb=" N ILE R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 322 " --> pdb=" O MET R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 363 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 364 through 367 Processing helix chain 'R' and resid 378 through 386 removed outlier: 3.761A pdb=" N VAL R 383 " --> pdb=" O ARG R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 417 removed outlier: 3.647A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.303A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.658A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.757A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.750A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.891A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.574A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.979A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.123A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 20 368 hydrogen bonds defined for protein. 1041 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: 1.06 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2586 1.35 - 1.47: 2005 1.47 - 1.59: 3510 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 8170 Sorted by residual: bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.459 1.493 -0.035 9.10e-03 1.21e+04 1.44e+01 bond pdb=" N VAL B 307 " pdb=" CA VAL B 307 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.17e+00 ... (remaining 8165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 10412 1.39 - 2.77: 551 2.77 - 4.16: 80 4.16 - 5.54: 12 5.54 - 6.93: 3 Bond angle restraints: 11058 Sorted by residual: angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 120.21 125.92 -5.71 9.60e-01 1.09e+00 3.53e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 108.75 4.72 1.01e+00 9.80e-01 2.18e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 111.28 106.73 4.55 1.09e+00 8.42e-01 1.74e+01 angle pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" O GLY B 272 " ideal model delta sigma weight residual 121.58 118.03 3.55 9.00e-01 1.23e+00 1.56e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 113.42 108.90 4.52 1.17e+00 7.31e-01 1.50e+01 ... (remaining 11053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4420 17.07 - 34.13: 325 34.13 - 51.20: 59 51.20 - 68.27: 9 68.27 - 85.34: 5 Dihedral angle restraints: 4818 sinusoidal: 1916 harmonic: 2902 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 42.60 50.40 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" C HIS B 311 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " pdb=" CB HIS B 311 " ideal model delta harmonic sigma weight residual -122.60 -131.68 9.08 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " pdb=" OD1 ASP B 186 " ideal model delta sinusoidal sigma weight residual -30.00 -90.69 60.69 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 4815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 968 0.053 - 0.105: 193 0.105 - 0.158: 43 0.158 - 0.210: 11 0.210 - 0.263: 9 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1221 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 297 " 0.025 2.00e-02 2.50e+03 1.92e-02 9.22e+00 pdb=" CG TRP R 297 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP R 297 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 297 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 297 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 297 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 297 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ILE R 205 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS R 206 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 311 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO R 312 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " 0.019 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1779 2.78 - 3.31: 7554 3.31 - 3.84: 13124 3.84 - 4.37: 17133 4.37 - 4.90: 28362 Nonbonded interactions: 67952 Sorted by model distance: nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.246 3.120 nonbonded pdb=" ND2 ASN R 320 " pdb=" O PHE R 362 " model vdw 2.257 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.262 3.040 nonbonded pdb=" O ASN B 293 " pdb=" ND2 ASN B 293 " model vdw 2.287 3.120 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.293 3.040 ... (remaining 67947 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.790 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.280 Find NCS groups from input model: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.005 0.048 8173 Z= 0.327 Angle : 0.681 6.926 11064 Z= 0.469 Chirality : 0.051 0.263 1224 Planarity : 0.003 0.034 1400 Dihedral : 12.481 85.336 2935 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.81 % Allowed : 3.59 % Favored : 95.60 % 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: -4.06 (0.23), residues: 974 helix: -3.63 (0.18), residues: 352 sheet: -2.19 (0.33), residues: 213 loop : -1.82 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.016 0.001 TYR R 157 PHE 0.014 0.001 PHE B 151 TRP 0.051 0.002 TRP R 297 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8170) covalent geometry : angle 0.68082 (11058) SS BOND : bond 0.00495 ( 3) SS BOND : angle 1.16629 ( 6) hydrogen bonds : bond 0.26998 ( 368) hydrogen bonds : angle 10.70582 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 20 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.7005 (ttp80) REVERT: A 34 LYS cc_start: 0.8235 (tttp) cc_final: 0.7970 (ttpt) REVERT: A 209 GLU cc_start: 0.7185 (tt0) cc_final: 0.6891 (tt0) REVERT: B 186 ASP cc_start: 0.7990 (p0) cc_final: 0.7490 (p0) REVERT: N 46 GLU cc_start: 0.8144 (pt0) cc_final: 0.7820 (mt-10) REVERT: R 378 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7659 (mtpp) REVERT: R 379 ARG cc_start: 0.7571 (mmm160) cc_final: 0.7362 (mmm160) outliers start: 7 outliers final: 3 residues processed: 146 average time/residue: 0.1215 time to fit residues: 22.0725 Evaluate side-chains 107 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 29 GLN A 278 ASN B 17 GLN B 32 GLN B 35 ASN B 293 ASN B 295 ASN N 120 GLN N 123 GLN P 1 HIS P 16 GLN R 240 ASN R 333 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125384 restraints weight = 8369.152| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.87 r_work: 0.3354 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8173 Z= 0.129 Angle : 0.547 6.248 11064 Z= 0.296 Chirality : 0.042 0.150 1224 Planarity : 0.004 0.038 1400 Dihedral : 4.706 33.316 1098 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 8.11 % Favored : 90.27 % 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: -2.19 (0.25), residues: 974 helix: -1.11 (0.26), residues: 360 sheet: -1.71 (0.34), residues: 213 loop : -1.41 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.023 0.001 TYR R 157 PHE 0.023 0.001 PHE A 212 TRP 0.030 0.002 TRP R 297 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8170) covalent geometry : angle 0.54625 (11058) SS BOND : bond 0.00437 ( 3) SS BOND : angle 1.20848 ( 6) hydrogen bonds : bond 0.04575 ( 368) hydrogen bonds : angle 5.73315 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6786 (mtm110) REVERT: A 34 LYS cc_start: 0.7992 (tttp) cc_final: 0.7608 (ttpt) REVERT: B 186 ASP cc_start: 0.8206 (p0) cc_final: 0.7941 (p0) REVERT: N 28 THR cc_start: 0.8275 (m) cc_final: 0.7962 (p) REVERT: N 46 GLU cc_start: 0.8395 (pt0) cc_final: 0.7710 (mt-10) REVERT: R 190 MET cc_start: 0.7384 (mtp) cc_final: 0.7070 (mtt) REVERT: R 230 MET cc_start: 0.7592 (mmp) cc_final: 0.7252 (mmp) REVERT: R 379 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7577 (mmm160) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.1098 time to fit residues: 18.7907 Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124571 restraints weight = 8410.940| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.88 r_work: 0.3345 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8173 Z= 0.149 Angle : 0.533 5.846 11064 Z= 0.287 Chirality : 0.042 0.164 1224 Planarity : 0.004 0.042 1400 Dihedral : 4.561 34.088 1097 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 11.36 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 974 helix: -0.30 (0.27), residues: 361 sheet: -1.53 (0.34), residues: 217 loop : -1.14 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 12 TYR 0.021 0.001 TYR R 157 PHE 0.021 0.001 PHE A 212 TRP 0.025 0.002 TRP R 297 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8170) covalent geometry : angle 0.53233 (11058) SS BOND : bond 0.00462 ( 3) SS BOND : angle 1.09845 ( 6) hydrogen bonds : bond 0.04082 ( 368) hydrogen bonds : angle 5.23077 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6982 (ttp-110) cc_final: 0.6688 (mtm110) REVERT: A 24 LYS cc_start: 0.7298 (tttm) cc_final: 0.6803 (mmtt) REVERT: A 34 LYS cc_start: 0.7953 (tttp) cc_final: 0.7585 (ttpt) REVERT: A 389 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7164 (ttm-80) REVERT: B 186 ASP cc_start: 0.8190 (p0) cc_final: 0.7942 (p0) REVERT: R 180 LYS cc_start: 0.7392 (tttp) cc_final: 0.7007 (ttpt) REVERT: R 190 MET cc_start: 0.7442 (mtp) cc_final: 0.7163 (mtt) REVERT: R 379 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7508 (mmm160) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 0.1141 time to fit residues: 18.7060 Evaluate side-chains 123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126823 restraints weight = 8522.389| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.91 r_work: 0.3378 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8173 Z= 0.111 Angle : 0.489 6.104 11064 Z= 0.264 Chirality : 0.041 0.154 1224 Planarity : 0.003 0.031 1400 Dihedral : 4.221 19.375 1095 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.20 % Allowed : 13.21 % Favored : 84.59 % 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: -0.95 (0.26), residues: 974 helix: 0.27 (0.27), residues: 362 sheet: -1.32 (0.34), residues: 207 loop : -0.93 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 12 TYR 0.019 0.001 TYR R 157 PHE 0.019 0.001 PHE A 212 TRP 0.027 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8170) covalent geometry : angle 0.48837 (11058) SS BOND : bond 0.00358 ( 3) SS BOND : angle 1.17784 ( 6) hydrogen bonds : bond 0.03499 ( 368) hydrogen bonds : angle 4.78598 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6904 (ttp-110) cc_final: 0.6601 (mtm110) REVERT: A 24 LYS cc_start: 0.7193 (tttm) cc_final: 0.6734 (mtmm) REVERT: A 34 LYS cc_start: 0.7892 (tttp) cc_final: 0.7561 (ttpt) REVERT: A 342 ARG cc_start: 0.7788 (ttt180) cc_final: 0.6957 (ttp-170) REVERT: A 389 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7093 (ttm-80) REVERT: B 98 SER cc_start: 0.8652 (m) cc_final: 0.8146 (t) REVERT: B 105 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8838 (t80) REVERT: R 180 LYS cc_start: 0.7323 (tttp) cc_final: 0.6971 (ttpt) REVERT: R 190 MET cc_start: 0.7480 (mtp) cc_final: 0.7198 (mtt) REVERT: R 378 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7304 (mtpp) REVERT: R 379 ARG cc_start: 0.7828 (mmm160) cc_final: 0.7497 (mmm160) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.1187 time to fit residues: 20.1596 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 32 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125150 restraints weight = 8542.608| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.91 r_work: 0.3354 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8173 Z= 0.127 Angle : 0.497 5.968 11064 Z= 0.269 Chirality : 0.041 0.155 1224 Planarity : 0.003 0.036 1400 Dihedral : 4.215 19.942 1095 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 14.14 % Favored : 83.78 % 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: -0.66 (0.27), residues: 974 helix: 0.54 (0.27), residues: 365 sheet: -1.23 (0.34), residues: 207 loop : -0.76 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 12 TYR 0.020 0.001 TYR R 157 PHE 0.017 0.001 PHE A 212 TRP 0.027 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8170) covalent geometry : angle 0.49622 (11058) SS BOND : bond 0.00278 ( 3) SS BOND : angle 1.04630 ( 6) hydrogen bonds : bond 0.03541 ( 368) hydrogen bonds : angle 4.62663 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6882 (ttp-110) cc_final: 0.6580 (mtm110) REVERT: A 24 LYS cc_start: 0.7210 (tttm) cc_final: 0.6759 (mtmm) REVERT: A 34 LYS cc_start: 0.7827 (tttp) cc_final: 0.7542 (ttpt) REVERT: B 98 SER cc_start: 0.8693 (m) cc_final: 0.8189 (t) REVERT: B 105 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8843 (t80) REVERT: R 180 LYS cc_start: 0.7292 (tttp) cc_final: 0.6953 (ttpt) REVERT: R 190 MET cc_start: 0.7518 (mtp) cc_final: 0.7197 (mtt) REVERT: R 378 LYS cc_start: 0.7534 (ttmt) cc_final: 0.7297 (mtpp) REVERT: R 379 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7516 (mmm160) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.1159 time to fit residues: 19.6009 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125550 restraints weight = 8400.741| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.89 r_work: 0.3356 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8173 Z= 0.122 Angle : 0.496 6.182 11064 Z= 0.268 Chirality : 0.041 0.154 1224 Planarity : 0.003 0.034 1400 Dihedral : 4.182 20.114 1095 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 14.95 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.27), residues: 974 helix: 0.76 (0.28), residues: 365 sheet: -1.13 (0.34), residues: 207 loop : -0.64 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 12 TYR 0.019 0.001 TYR R 157 PHE 0.020 0.001 PHE A 212 TRP 0.027 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8170) covalent geometry : angle 0.49576 (11058) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.14182 ( 6) hydrogen bonds : bond 0.03477 ( 368) hydrogen bonds : angle 4.53269 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6886 (ttp-110) cc_final: 0.6509 (mtm110) REVERT: A 24 LYS cc_start: 0.7194 (tttm) cc_final: 0.6706 (mtmm) REVERT: A 34 LYS cc_start: 0.7795 (tttp) cc_final: 0.7482 (ttpt) REVERT: A 342 ARG cc_start: 0.7777 (ttt180) cc_final: 0.6960 (ttp-170) REVERT: B 98 SER cc_start: 0.8683 (m) cc_final: 0.8180 (t) REVERT: B 105 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8860 (t80) REVERT: P 12 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7897 (ttm-80) REVERT: R 180 LYS cc_start: 0.7287 (tttp) cc_final: 0.6960 (ttpt) REVERT: R 190 MET cc_start: 0.7501 (mtp) cc_final: 0.7169 (mtt) REVERT: R 378 LYS cc_start: 0.7496 (ttmt) cc_final: 0.7276 (mtpp) REVERT: R 379 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7526 (mmm160) REVERT: R 380 GLU cc_start: 0.8147 (pm20) cc_final: 0.7935 (pm20) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.1137 time to fit residues: 19.1313 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126083 restraints weight = 8447.563| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.90 r_work: 0.3354 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8173 Z= 0.117 Angle : 0.490 6.091 11064 Z= 0.265 Chirality : 0.041 0.152 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.141 20.195 1095 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.32 % Allowed : 16.11 % Favored : 81.58 % 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: -0.26 (0.27), residues: 974 helix: 0.91 (0.28), residues: 365 sheet: -1.06 (0.34), residues: 207 loop : -0.54 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.019 0.001 TYR R 157 PHE 0.020 0.001 PHE A 212 TRP 0.023 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8170) covalent geometry : angle 0.48928 (11058) SS BOND : bond 0.00294 ( 3) SS BOND : angle 1.04709 ( 6) hydrogen bonds : bond 0.03408 ( 368) hydrogen bonds : angle 4.40337 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6500 (mtm110) REVERT: A 24 LYS cc_start: 0.7172 (tttm) cc_final: 0.6687 (mtmm) REVERT: A 34 LYS cc_start: 0.7785 (tttp) cc_final: 0.7482 (ttpt) REVERT: A 342 ARG cc_start: 0.7758 (ttt180) cc_final: 0.6969 (ttp-170) REVERT: A 389 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7390 (ttm-80) REVERT: B 98 SER cc_start: 0.8693 (m) cc_final: 0.8197 (t) REVERT: B 105 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8855 (t80) REVERT: R 180 LYS cc_start: 0.7284 (tttp) cc_final: 0.6969 (ttpt) REVERT: R 190 MET cc_start: 0.7501 (mtp) cc_final: 0.7163 (mtt) REVERT: R 257 GLU cc_start: 0.7487 (tp30) cc_final: 0.7255 (tt0) REVERT: R 378 LYS cc_start: 0.7516 (ttmt) cc_final: 0.7295 (mtpp) REVERT: R 379 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7505 (mmm160) REVERT: R 380 GLU cc_start: 0.8144 (pm20) cc_final: 0.7902 (pm20) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.1196 time to fit residues: 20.4313 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 36 optimal weight: 0.0870 chunk 77 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126982 restraints weight = 8461.895| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8173 Z= 0.112 Angle : 0.496 6.581 11064 Z= 0.268 Chirality : 0.043 0.397 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.095 20.134 1095 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.32 % Allowed : 16.69 % Favored : 81.00 % 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: -0.11 (0.27), residues: 974 helix: 1.02 (0.28), residues: 365 sheet: -0.96 (0.34), residues: 207 loop : -0.47 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 12 TYR 0.020 0.001 TYR N 60 PHE 0.019 0.001 PHE A 212 TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8170) covalent geometry : angle 0.49541 (11058) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.04898 ( 6) hydrogen bonds : bond 0.03345 ( 368) hydrogen bonds : angle 4.33989 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.242 Fit side-chains REVERT: A 20 ARG cc_start: 0.6835 (ttp-110) cc_final: 0.6458 (mtm110) REVERT: A 24 LYS cc_start: 0.7134 (tttm) cc_final: 0.6682 (mtmm) REVERT: A 27 GLU cc_start: 0.7730 (tp30) cc_final: 0.6905 (mp0) REVERT: A 34 LYS cc_start: 0.7729 (tttp) cc_final: 0.7428 (ttpt) REVERT: A 314 GLU cc_start: 0.7180 (mp0) cc_final: 0.6907 (mp0) REVERT: A 342 ARG cc_start: 0.7745 (ttt180) cc_final: 0.6950 (ttp-170) REVERT: A 389 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7341 (ttm-80) REVERT: B 98 SER cc_start: 0.8720 (m) cc_final: 0.8239 (t) REVERT: B 105 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8943 (t80) REVERT: N 28 THR cc_start: 0.8491 (t) cc_final: 0.8175 (m) REVERT: R 180 LYS cc_start: 0.7244 (tttp) cc_final: 0.6941 (ttpt) REVERT: R 190 MET cc_start: 0.7510 (mtp) cc_final: 0.7189 (mtt) REVERT: R 257 GLU cc_start: 0.7475 (tp30) cc_final: 0.7267 (tt0) REVERT: R 378 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7303 (mtpp) REVERT: R 379 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7510 (mmm160) outliers start: 20 outliers final: 18 residues processed: 130 average time/residue: 0.1132 time to fit residues: 18.9126 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126587 restraints weight = 8386.341| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.89 r_work: 0.3359 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8173 Z= 0.122 Angle : 0.501 6.548 11064 Z= 0.271 Chirality : 0.043 0.355 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.119 20.218 1095 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.55 % Allowed : 16.92 % Favored : 80.53 % 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: -0.03 (0.28), residues: 974 helix: 1.06 (0.28), residues: 365 sheet: -0.85 (0.35), residues: 205 loop : -0.44 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 12 TYR 0.020 0.001 TYR N 60 PHE 0.022 0.001 PHE A 212 TRP 0.022 0.001 TRP R 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8170) covalent geometry : angle 0.50023 (11058) SS BOND : bond 0.00276 ( 3) SS BOND : angle 1.02610 ( 6) hydrogen bonds : bond 0.03370 ( 368) hydrogen bonds : angle 4.33617 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.305 Fit side-chains REVERT: A 20 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6523 (mtm110) REVERT: A 24 LYS cc_start: 0.7159 (tttm) cc_final: 0.6702 (mtmm) REVERT: A 27 GLU cc_start: 0.7729 (tp30) cc_final: 0.6915 (mp0) REVERT: A 34 LYS cc_start: 0.7741 (tttp) cc_final: 0.7437 (ttpt) REVERT: A 314 GLU cc_start: 0.7166 (mp0) cc_final: 0.6835 (mp0) REVERT: A 342 ARG cc_start: 0.7758 (ttt180) cc_final: 0.6982 (ttp-170) REVERT: A 389 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7328 (ttm-80) REVERT: B 98 SER cc_start: 0.8734 (m) cc_final: 0.8266 (t) REVERT: B 105 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8962 (t80) REVERT: N 28 THR cc_start: 0.8540 (t) cc_final: 0.8226 (m) REVERT: R 180 LYS cc_start: 0.7270 (tttp) cc_final: 0.6968 (ttpt) REVERT: R 190 MET cc_start: 0.7526 (mtp) cc_final: 0.7193 (mtt) REVERT: R 378 LYS cc_start: 0.7502 (ttmt) cc_final: 0.7256 (mtpp) REVERT: R 379 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7495 (mmm160) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.1144 time to fit residues: 19.6085 Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 0.0570 chunk 81 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127009 restraints weight = 8428.431| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.89 r_work: 0.3374 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8173 Z= 0.116 Angle : 0.499 6.422 11064 Z= 0.270 Chirality : 0.042 0.342 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.092 20.298 1095 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.55 % Allowed : 17.15 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 974 helix: 1.13 (0.28), residues: 365 sheet: -0.79 (0.34), residues: 211 loop : -0.38 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 12 TYR 0.019 0.001 TYR R 157 PHE 0.020 0.001 PHE A 212 TRP 0.021 0.001 TRP R 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8170) covalent geometry : angle 0.49860 (11058) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.03172 ( 6) hydrogen bonds : bond 0.03312 ( 368) hydrogen bonds : angle 4.29957 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.590 Fit side-chains REVERT: A 20 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.6338 (mtm110) REVERT: A 24 LYS cc_start: 0.7151 (tttm) cc_final: 0.6663 (mmtm) REVERT: A 27 GLU cc_start: 0.7707 (tp30) cc_final: 0.6917 (mp0) REVERT: A 34 LYS cc_start: 0.7714 (tttp) cc_final: 0.7403 (ttpt) REVERT: A 314 GLU cc_start: 0.7118 (mp0) cc_final: 0.6820 (mp0) REVERT: A 342 ARG cc_start: 0.7752 (ttt180) cc_final: 0.6964 (ttp-170) REVERT: A 389 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7363 (ttm-80) REVERT: B 98 SER cc_start: 0.8737 (m) cc_final: 0.8278 (t) REVERT: B 105 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8961 (t80) REVERT: N 28 THR cc_start: 0.8519 (t) cc_final: 0.8204 (m) REVERT: R 180 LYS cc_start: 0.7257 (tttp) cc_final: 0.6950 (ttpt) REVERT: R 190 MET cc_start: 0.7546 (mtp) cc_final: 0.7209 (mtt) REVERT: R 378 LYS cc_start: 0.7395 (ttmt) cc_final: 0.7146 (mtpp) REVERT: R 379 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7404 (mmm160) outliers start: 22 outliers final: 20 residues processed: 134 average time/residue: 0.1120 time to fit residues: 19.3895 Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127198 restraints weight = 8373.960| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.88 r_work: 0.3376 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 8173 Z= 0.148 Angle : 0.936 59.195 11064 Z= 0.531 Chirality : 0.057 1.365 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.089 20.345 1095 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.43 % Allowed : 17.15 % Favored : 80.42 % Cbeta Deviations : 0.11 % 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: 0.07 (0.28), residues: 974 helix: 1.15 (0.28), residues: 365 sheet: -0.78 (0.34), residues: 211 loop : -0.38 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 12 TYR 0.019 0.001 TYR R 157 PHE 0.020 0.001 PHE A 212 TRP 0.022 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8170) covalent geometry : angle 0.93595 (11058) SS BOND : bond 0.00239 ( 3) SS BOND : angle 1.02778 ( 6) hydrogen bonds : bond 0.03304 ( 368) hydrogen bonds : angle 4.29869 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.87 seconds wall clock time: 40 minutes 15.49 seconds (2415.49 seconds total)