Starting phenix.real_space_refine on Tue Sep 24 11:36:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_20278.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_20278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_20278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_20278.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/09_2024/6p9y_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.27, per 1000 atoms: 0.66 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 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: 0.92 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: 2.26 Time building geometry restraints manager: 2.11 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: 1.920 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.939 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: 0.2963 time to fit residues: 53.7404 Evaluate side-chains 107 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7231 (tttm) cc_final: 0.7019 (mmtt) REVERT: A 34 LYS cc_start: 0.7980 (tttp) cc_final: 0.7773 (ttpt) REVERT: N 46 GLU cc_start: 0.8054 (pt0) cc_final: 0.7699 (mt-10) REVERT: R 230 MET cc_start: 0.7498 (mmp) cc_final: 0.7168 (mmp) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.2580 time to fit residues: 44.2378 Evaluate side-chains 117 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8170 Z= 0.206 Angle : 0.528 6.216 11058 Z= 0.284 Chirality : 0.042 0.166 1224 Planarity : 0.004 0.039 1400 Dihedral : 4.447 30.417 1096 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.20 % Allowed : 11.12 % Favored : 86.67 % 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: -1.41 (0.26), residues: 974 helix: -0.28 (0.27), residues: 362 sheet: -1.50 (0.34), residues: 217 loop : -1.03 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.021 0.001 TYR R 157 ARG 0.002 0.000 ARG P 12 *********************** 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 144 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7191 (tttm) cc_final: 0.6977 (mmtt) REVERT: A 342 ARG cc_start: 0.7600 (ttt180) cc_final: 0.6993 (ttp-170) REVERT: A 389 ARG cc_start: 0.7178 (ttm-80) cc_final: 0.6860 (ttm-80) REVERT: R 180 LYS cc_start: 0.7540 (tttp) cc_final: 0.7306 (ttpt) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.2713 time to fit residues: 46.1602 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8170 Z= 0.197 Angle : 0.511 6.112 11058 Z= 0.276 Chirality : 0.042 0.285 1224 Planarity : 0.003 0.037 1400 Dihedral : 4.416 31.677 1096 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.55 % Allowed : 12.98 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.26), residues: 974 helix: 0.21 (0.27), residues: 363 sheet: -1.34 (0.34), residues: 207 loop : -0.93 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 297 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.021 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 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7148 (tttm) cc_final: 0.6943 (mmtt) REVERT: A 342 ARG cc_start: 0.7571 (ttt180) cc_final: 0.6973 (ttp-110) REVERT: B 105 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8722 (t80) REVERT: R 180 LYS cc_start: 0.7519 (tttp) cc_final: 0.7303 (ttpt) outliers start: 22 outliers final: 14 residues processed: 128 average time/residue: 0.2642 time to fit residues: 43.1815 Evaluate side-chains 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 41 HIS A 213 GLN A 278 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8170 Z= 0.187 Angle : 0.501 6.173 11058 Z= 0.271 Chirality : 0.042 0.300 1224 Planarity : 0.003 0.036 1400 Dihedral : 4.359 31.830 1096 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.85 % Allowed : 14.37 % 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 (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: -0.70 (0.27), residues: 974 helix: 0.47 (0.28), residues: 365 sheet: -1.22 (0.34), residues: 207 loop : -0.76 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.020 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 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6523 (mtm110) cc_final: 0.6174 (mtm-85) REVERT: A 24 LYS cc_start: 0.7125 (tttm) cc_final: 0.6754 (mtmm) REVERT: A 342 ARG cc_start: 0.7562 (ttt180) cc_final: 0.6997 (ttp-170) REVERT: B 98 SER cc_start: 0.8483 (m) cc_final: 0.8132 (t) REVERT: B 105 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8741 (t80) REVERT: N 28 THR cc_start: 0.8623 (t) cc_final: 0.8404 (m) REVERT: R 180 LYS cc_start: 0.7494 (tttp) cc_final: 0.7292 (ttpt) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 0.2529 time to fit residues: 40.5048 Evaluate side-chains 123 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2566 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= 0.171 Angle : 0.495 6.071 11058 Z= 0.268 Chirality : 0.042 0.256 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.302 31.550 1096 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.20 % Allowed : 15.18 % 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 (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: -0.48 (0.27), residues: 974 helix: 0.65 (0.28), residues: 369 sheet: -1.10 (0.34), residues: 207 loop : -0.65 (0.31), 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 0.021 0.001 PHE A 222 TYR 0.019 0.001 TYR R 157 ARG 0.004 0.000 ARG P 12 *********************** 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 138 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6457 (mtm110) cc_final: 0.6101 (mtm-85) REVERT: A 24 LYS cc_start: 0.7103 (tttm) cc_final: 0.6794 (mtmm) REVERT: A 342 ARG cc_start: 0.7548 (ttt180) cc_final: 0.6992 (ttp-170) REVERT: A 389 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6949 (ttm-80) REVERT: B 98 SER cc_start: 0.8469 (m) cc_final: 0.8113 (t) REVERT: P 12 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7674 (ttm-80) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.2514 time to fit residues: 42.5856 Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 0.0370 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 293 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8170 Z= 0.136 Angle : 0.478 5.954 11058 Z= 0.260 Chirality : 0.041 0.151 1224 Planarity : 0.003 0.031 1400 Dihedral : 4.161 28.972 1096 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.97 % Allowed : 16.57 % Favored : 81.46 % 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: -0.21 (0.27), residues: 974 helix: 0.84 (0.28), residues: 371 sheet: -0.97 (0.34), residues: 207 loop : -0.46 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 297 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.022 0.001 TYR N 60 ARG 0.003 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 143 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.925 Fit side-chains REVERT: A 20 ARG cc_start: 0.6451 (mtm110) cc_final: 0.6097 (mtm-85) REVERT: A 24 LYS cc_start: 0.7035 (tttm) cc_final: 0.6731 (mtmm) REVERT: A 342 ARG cc_start: 0.7508 (ttt180) cc_final: 0.6973 (ttp-170) REVERT: B 98 SER cc_start: 0.8481 (m) cc_final: 0.8186 (t) REVERT: P 12 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7669 (ttm-80) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.2449 time to fit residues: 42.9476 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 175 GLN Chi-restraints excluded: chain B residue 196 THR 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 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 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 31 GLN A 278 ASN A 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2785 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= 0.181 Angle : 0.509 7.082 11058 Z= 0.275 Chirality : 0.042 0.150 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.239 28.554 1096 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 (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: -0.17 (0.27), residues: 974 helix: 0.91 (0.28), residues: 369 sheet: -0.94 (0.34), residues: 207 loop : -0.47 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.020 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 fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7047 (tttm) cc_final: 0.6739 (mtmm) REVERT: A 342 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7003 (ttp-170) REVERT: A 389 ARG cc_start: 0.7253 (ttm110) cc_final: 0.6906 (ttm-80) REVERT: B 98 SER cc_start: 0.8492 (m) cc_final: 0.8141 (t) outliers start: 20 outliers final: 18 residues processed: 128 average time/residue: 0.2581 time to fit residues: 42.7270 Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASN 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 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 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 278 ASN A 371 ASN R 182 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8170 Z= 0.198 Angle : 0.521 6.886 11058 Z= 0.282 Chirality : 0.043 0.149 1224 Planarity : 0.003 0.036 1400 Dihedral : 4.289 29.554 1096 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.20 % Allowed : 17.15 % Favored : 80.65 % 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: -0.14 (0.27), residues: 974 helix: 0.93 (0.28), residues: 369 sheet: -0.91 (0.34), residues: 207 loop : -0.46 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.001 PHE A 212 TYR 0.020 0.001 TYR R 157 ARG 0.004 0.000 ARG P 12 *********************** 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 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.914 Fit side-chains REVERT: A 20 ARG cc_start: 0.6492 (mtm110) cc_final: 0.6142 (mtm-85) REVERT: A 24 LYS cc_start: 0.7087 (tttm) cc_final: 0.6724 (mtmm) REVERT: A 342 ARG cc_start: 0.7556 (ttt180) cc_final: 0.7002 (ttp-170) REVERT: A 389 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6916 (ttm-80) REVERT: B 98 SER cc_start: 0.8502 (m) cc_final: 0.8169 (t) outliers start: 19 outliers final: 17 residues processed: 126 average time/residue: 0.2602 time to fit residues: 42.1035 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASN 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 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 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 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 31 GLN A 278 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2860 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= 0.184 Angle : 0.521 6.797 11058 Z= 0.282 Chirality : 0.042 0.182 1224 Planarity : 0.003 0.034 1400 Dihedral : 4.300 29.216 1096 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 17.50 % Favored : 80.42 % 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: -0.01 (0.28), residues: 974 helix: 1.05 (0.28), residues: 365 sheet: -0.81 (0.34), residues: 211 loop : -0.41 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.025 0.001 PHE A 212 TYR 0.020 0.001 TYR R 157 ARG 0.005 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 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.865 Fit side-chains REVERT: A 20 ARG cc_start: 0.6490 (mtm110) cc_final: 0.6140 (mtm-85) REVERT: A 24 LYS cc_start: 0.7037 (tttm) cc_final: 0.6676 (mtmm) REVERT: A 342 ARG cc_start: 0.7535 (ttt180) cc_final: 0.6980 (ttp-170) REVERT: A 389 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6906 (ttm-80) REVERT: B 98 SER cc_start: 0.8523 (m) cc_final: 0.8199 (t) outliers start: 18 outliers final: 17 residues processed: 124 average time/residue: 0.2471 time to fit residues: 39.7304 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASN 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 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 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 278 ASN A 371 ASN B 32 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126330 restraints weight = 8407.557| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.89 r_work: 0.3368 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2905 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= 0.177 Angle : 0.524 6.597 11058 Z= 0.285 Chirality : 0.044 0.421 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.289 29.145 1096 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 17.50 % 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: 0.01 (0.28), residues: 974 helix: 1.04 (0.28), residues: 369 sheet: -0.77 (0.35), residues: 211 loop : -0.39 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 297 HIS 0.010 0.001 HIS A 220 PHE 0.024 0.001 PHE A 212 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: 2235.81 seconds wall clock time: 40 minutes 14.72 seconds (2414.72 seconds total)