Starting phenix.real_space_refine on Wed Mar 12 13:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p9y_20278/03_2025/6p9y_20278.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p9y_20278/03_2025/6p9y_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_2025/6p9y_20278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2025/6p9y_20278.map" model { file = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2025/6p9y_20278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p9y_20278/03_2025/6p9y_20278.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.10, per 1000 atoms: 0.64 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.41 Time building geometry restraints manager: 2.15 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: 0.010 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- 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 8170 Z= 0.326 Angle : 0.681 6.926 11058 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.051 0.002 TRP R 297 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.016 0.001 TYR R 157 ARG 0.004 0.000 ARG N 98 *********************** 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 : 0.927 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: 0.6717 (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: 0.3044 time to fit residues: 55.4252 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 : 0.848 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 35 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.159572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126582 restraints weight = 8279.140| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.86 r_work: 0.3370 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8170 Z= 0.170 Angle : 0.542 6.411 11058 Z= 0.293 Chirality : 0.042 0.153 1224 Planarity : 0.004 0.034 1400 Dihedral : 4.663 32.752 1098 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.16 % Allowed : 8.34 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.25), residues: 974 helix: -1.13 (0.26), residues: 360 sheet: -1.73 (0.34), residues: 213 loop : -1.38 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 297 HIS 0.005 0.001 HIS B 311 PHE 0.022 0.001 PHE A 212 TYR 0.024 0.001 TYR R 157 ARG 0.004 0.000 ARG A 336 *********************** 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 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7024 (ttp-110) cc_final: 0.6756 (mtm110) REVERT: A 24 LYS cc_start: 0.7342 (tttm) cc_final: 0.6847 (mmtt) REVERT: A 34 LYS cc_start: 0.7977 (tttp) cc_final: 0.7598 (ttpt) REVERT: A 386 MET cc_start: 0.8544 (ttp) cc_final: 0.8236 (ptm) REVERT: B 186 ASP cc_start: 0.8181 (p0) cc_final: 0.7930 (p0) REVERT: N 28 THR cc_start: 0.8244 (m) cc_final: 0.7953 (p) REVERT: N 46 GLU cc_start: 0.8362 (pt0) cc_final: 0.7674 (mt-10) REVERT: R 190 MET cc_start: 0.7347 (mtp) cc_final: 0.7026 (mtt) REVERT: R 230 MET cc_start: 0.7540 (mmp) cc_final: 0.7239 (mmp) REVERT: R 379 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7560 (mmm160) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.2606 time to fit residues: 44.7348 Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET 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 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122951 restraints weight = 8593.389| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8170 Z= 0.256 Angle : 0.547 6.023 11058 Z= 0.294 Chirality : 0.043 0.171 1224 Planarity : 0.004 0.049 1400 Dihedral : 4.582 32.177 1096 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 11.47 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.26), residues: 974 helix: -0.30 (0.27), residues: 361 sheet: -1.53 (0.34), residues: 217 loop : -1.09 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 297 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.002 PHE A 212 TYR 0.022 0.001 TYR R 157 ARG 0.003 0.000 ARG B 304 *********************** 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 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6708 (mtm110) REVERT: A 24 LYS cc_start: 0.7341 (tttm) cc_final: 0.6832 (mmtt) REVERT: A 34 LYS cc_start: 0.7960 (tttp) cc_final: 0.7623 (ttpt) REVERT: A 389 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7166 (ttm-80) REVERT: B 186 ASP cc_start: 0.8187 (p0) cc_final: 0.7922 (p0) REVERT: R 180 LYS cc_start: 0.7351 (tttp) cc_final: 0.6984 (ttpt) REVERT: R 190 MET cc_start: 0.7532 (mtp) cc_final: 0.7279 (mtt) REVERT: R 227 LYS cc_start: 0.7457 (mttm) cc_final: 0.7231 (mmtp) REVERT: R 379 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7512 (mmm160) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.2741 time to fit residues: 45.2200 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 294 CYS Chi-restraints excluded: chain B residue 336 LEU 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 74 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125335 restraints weight = 8395.386| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.88 r_work: 0.3353 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.166 Angle : 0.493 5.842 11058 Z= 0.266 Chirality : 0.041 0.157 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.371 30.513 1096 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.78 % Allowed : 12.86 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 974 helix: 0.25 (0.27), residues: 362 sheet: -1.35 (0.34), residues: 207 loop : -0.93 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.003 0.000 ARG P 12 *********************** 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 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6916 (ttp-110) cc_final: 0.6618 (mtm110) REVERT: A 24 LYS cc_start: 0.7202 (tttm) cc_final: 0.6743 (mtmm) REVERT: A 34 LYS cc_start: 0.7909 (tttp) cc_final: 0.7623 (ttpt) REVERT: A 356 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6956 (ptt180) REVERT: R 180 LYS cc_start: 0.7266 (tttp) cc_final: 0.6920 (ttpt) REVERT: R 190 MET cc_start: 0.7500 (mtp) cc_final: 0.7202 (mtt) REVERT: R 230 MET cc_start: 0.7595 (mmp) cc_final: 0.7008 (mmp) REVERT: R 378 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7297 (mtpp) REVERT: R 379 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7469 (mmm160) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 0.2760 time to fit residues: 48.1303 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP 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 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 1 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 92 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.156964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123469 restraints weight = 8427.174| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.89 r_work: 0.3331 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8170 Z= 0.215 Angle : 0.512 5.934 11058 Z= 0.277 Chirality : 0.042 0.156 1224 Planarity : 0.003 0.042 1400 Dihedral : 4.439 32.834 1096 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 14.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 974 helix: 0.48 (0.27), residues: 364 sheet: -1.26 (0.34), residues: 207 loop : -0.79 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.021 0.001 TYR R 157 ARG 0.003 0.000 ARG P 12 *********************** 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 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6594 (mtm110) REVERT: A 24 LYS cc_start: 0.7251 (tttm) cc_final: 0.6799 (mtmm) REVERT: A 34 LYS cc_start: 0.7864 (tttp) cc_final: 0.7548 (ttpt) REVERT: A 356 ARG cc_start: 0.7556 (mtm180) cc_final: 0.6948 (ptt180) REVERT: N 28 THR cc_start: 0.8233 (m) cc_final: 0.8029 (p) REVERT: P 12 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.8009 (ttm-80) REVERT: R 180 LYS cc_start: 0.7288 (tttp) cc_final: 0.6937 (ttpt) REVERT: R 190 MET cc_start: 0.7487 (mtp) cc_final: 0.7145 (mtt) REVERT: R 227 LYS cc_start: 0.7568 (mttm) cc_final: 0.7332 (mmtp) REVERT: R 379 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7519 (mmm160) outliers start: 21 outliers final: 18 residues processed: 128 average time/residue: 0.2768 time to fit residues: 45.0009 Evaluate side-chains 125 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP 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 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124610 restraints weight = 8344.292| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.88 r_work: 0.3345 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.184 Angle : 0.497 5.812 11058 Z= 0.270 Chirality : 0.041 0.155 1224 Planarity : 0.003 0.037 1400 Dihedral : 4.359 31.766 1096 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 15.06 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 974 helix: 0.75 (0.28), residues: 364 sheet: -1.18 (0.34), residues: 207 loop : -0.65 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE A 222 TYR 0.019 0.001 TYR N 60 ARG 0.002 0.000 ARG B 134 *********************** 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 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6900 (ttp-110) cc_final: 0.6532 (mtm110) REVERT: A 24 LYS cc_start: 0.7214 (tttm) cc_final: 0.6749 (mtmm) REVERT: A 34 LYS cc_start: 0.7797 (tttp) cc_final: 0.7506 (ttpt) REVERT: A 389 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7363 (ttm-80) REVERT: B 105 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8613 (t80) REVERT: P 12 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: R 180 LYS cc_start: 0.7249 (tttp) cc_final: 0.6899 (ttpt) REVERT: R 190 MET cc_start: 0.7474 (mtp) cc_final: 0.7139 (mtt) REVERT: R 378 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7270 (mtpp) REVERT: R 379 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7510 (mmm160) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.2604 time to fit residues: 43.3731 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 65 THR 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 297 TRP 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 26 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123701 restraints weight = 8448.710| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.89 r_work: 0.3321 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8170 Z= 0.210 Angle : 0.508 5.905 11058 Z= 0.274 Chirality : 0.042 0.154 1224 Planarity : 0.003 0.039 1400 Dihedral : 4.385 32.513 1096 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.55 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 974 helix: 0.76 (0.28), residues: 369 sheet: -1.15 (0.34), residues: 207 loop : -0.58 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.020 0.001 TYR R 157 ARG 0.002 0.000 ARG B 134 *********************** 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 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6513 (mtm110) REVERT: A 24 LYS cc_start: 0.7247 (tttm) cc_final: 0.6742 (mtmm) REVERT: A 34 LYS cc_start: 0.7820 (tttp) cc_final: 0.7508 (ttpt) REVERT: A 389 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7346 (ttm-80) REVERT: B 105 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8679 (t80) REVERT: P 12 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: R 180 LYS cc_start: 0.7267 (tttp) cc_final: 0.6918 (ttpt) REVERT: R 190 MET cc_start: 0.7500 (mtp) cc_final: 0.7161 (mtt) REVERT: R 378 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7200 (mtpp) REVERT: R 379 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7512 (mmm160) outliers start: 22 outliers final: 19 residues processed: 127 average time/residue: 0.2604 time to fit residues: 42.7488 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 205 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124961 restraints weight = 8451.246| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.89 r_work: 0.3340 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.181 Angle : 0.502 7.098 11058 Z= 0.271 Chirality : 0.041 0.152 1224 Planarity : 0.003 0.034 1400 Dihedral : 4.314 31.810 1096 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.55 % Allowed : 17.38 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 974 helix: 0.88 (0.28), residues: 369 sheet: -1.08 (0.34), residues: 207 loop : -0.52 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.003 0.000 ARG B 134 *********************** 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 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6907 (ttp-110) cc_final: 0.6386 (mtm110) REVERT: A 24 LYS cc_start: 0.7205 (tttm) cc_final: 0.6714 (mtmm) REVERT: A 34 LYS cc_start: 0.7778 (tttp) cc_final: 0.7482 (ttpt) REVERT: A 389 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7337 (ttm-80) REVERT: B 98 SER cc_start: 0.8718 (m) cc_final: 0.8226 (t) REVERT: B 105 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8655 (t80) REVERT: P 12 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: R 180 LYS cc_start: 0.7261 (tttp) cc_final: 0.6942 (ttpt) REVERT: R 190 MET cc_start: 0.7481 (mtp) cc_final: 0.7164 (mtt) REVERT: R 257 GLU cc_start: 0.7450 (tp30) cc_final: 0.7243 (tt0) REVERT: R 378 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7178 (mtpp) REVERT: R 379 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7462 (mmm160) outliers start: 22 outliers final: 19 residues processed: 125 average time/residue: 0.2423 time to fit residues: 39.5956 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 205 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127036 restraints weight = 8475.168| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.89 r_work: 0.3376 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8170 Z= 0.150 Angle : 0.491 6.991 11058 Z= 0.266 Chirality : 0.042 0.370 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.185 30.500 1096 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.32 % Allowed : 17.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 974 helix: 1.04 (0.28), residues: 369 sheet: -0.99 (0.35), residues: 207 loop : -0.47 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.004 0.000 ARG B 134 *********************** 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 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6874 (ttp-110) cc_final: 0.6404 (mtm-85) REVERT: A 24 LYS cc_start: 0.7186 (tttm) cc_final: 0.6713 (mtmm) REVERT: A 34 LYS cc_start: 0.7710 (tttp) cc_final: 0.7410 (ttpt) REVERT: A 213 GLN cc_start: 0.8317 (tt0) cc_final: 0.8078 (tt0) REVERT: A 342 ARG cc_start: 0.7725 (ttt180) cc_final: 0.6939 (ttp-170) REVERT: A 389 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7336 (ttm-80) REVERT: B 98 SER cc_start: 0.8739 (m) cc_final: 0.8266 (t) REVERT: B 105 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8692 (t80) REVERT: N 28 THR cc_start: 0.8490 (t) cc_final: 0.8152 (m) REVERT: R 180 LYS cc_start: 0.7222 (tttp) cc_final: 0.6952 (ttpt) REVERT: R 190 MET cc_start: 0.7486 (mtp) cc_final: 0.7147 (mtt) REVERT: R 378 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7141 (mtpp) REVERT: R 379 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7492 (mmm160) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.2574 time to fit residues: 44.4519 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 205 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 390 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 = 0.3873 r_free = 0.3873 target = 0.159403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126242 restraints weight = 8411.856| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.89 r_work: 0.3366 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8170 Z= 0.176 Angle : 0.501 6.768 11058 Z= 0.271 Chirality : 0.043 0.396 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.218 31.121 1096 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 17.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 974 helix: 1.06 (0.28), residues: 369 sheet: -0.90 (0.35), residues: 205 loop : -0.46 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.004 0.000 ARG P 12 ********************** 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 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.6334 (mtm110) REVERT: A 24 LYS cc_start: 0.7113 (tttm) cc_final: 0.6591 (mmtm) REVERT: A 34 LYS cc_start: 0.7727 (tttp) cc_final: 0.7434 (ttpt) REVERT: A 342 ARG cc_start: 0.7734 (ttt180) cc_final: 0.6953 (ttp-170) REVERT: A 389 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7311 (ttm-80) REVERT: B 98 SER cc_start: 0.8738 (m) cc_final: 0.8273 (t) REVERT: B 105 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8590 (t80) REVERT: R 180 LYS cc_start: 0.7234 (tttp) cc_final: 0.6931 (ttpt) REVERT: R 190 MET cc_start: 0.7521 (mtp) cc_final: 0.7177 (mtt) REVERT: R 378 LYS cc_start: 0.7399 (ttmt) cc_final: 0.7147 (mtpp) REVERT: R 379 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7485 (mmm160) outliers start: 20 outliers final: 18 residues processed: 127 average time/residue: 0.2461 time to fit residues: 40.7899 Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 205 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.1980 chunk 78 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.158126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125212 restraints weight = 8464.890| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.87 r_work: 0.3364 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.182 Angle : 0.514 6.644 11058 Z= 0.279 Chirality : 0.044 0.516 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.241 31.030 1096 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.55 % Allowed : 17.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 974 helix: 1.07 (0.28), residues: 369 sheet: -0.91 (0.35), residues: 205 loop : -0.48 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE A 222 TYR 0.019 0.001 TYR R 157 ARG 0.004 0.000 ARG P 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.56 seconds wall clock time: 85 minutes 30.26 seconds (5130.26 seconds total)