Starting phenix.real_space_refine on Thu Mar 13 19:52:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270.map" model { file = "/net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sai_40270/03_2025/8sai_40270_neut.cif" } resolution = 3.27 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= 0.009 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 68 5.16 5 C 5774 2.51 5 N 1534 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 9062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2373 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1824 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Classifications: {'peptide': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.65 Number of scatterers: 9062 At special positions: 0 Unit cell: (92, 121.44, 132.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 1 15.00 O 1685 8.00 N 1534 7.00 C 5774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 2.11 Conformation dependent library (CDL) restraints added in 953.2 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 36.3% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 53 through 75 removed outlier: 3.603A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 118 removed outlier: 3.655A pdb=" N CYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.550A pdb=" N ASN A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 159 removed outlier: 3.878A pdb=" N CYS A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 197 removed outlier: 3.854A pdb=" N TYR A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 250 removed outlier: 3.522A pdb=" N ASN A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.645A pdb=" N VAL A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 3.814A pdb=" N HIS A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 331 Proline residue: A 324 - end of helix removed outlier: 4.469A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'C' and resid 7 through 22 removed outlier: 3.922A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.525A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'D' and resid 6 through 28 removed outlier: 3.579A pdb=" N LYS D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.574A pdb=" N MET D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.378A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 Processing helix chain 'D' and resid 270 through 279 removed outlier: 4.637A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 327 through 352 removed outlier: 3.908A pdb=" N ASN D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.523A pdb=" N CYS E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.841A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.713A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 224 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 47 through 52 removed outlier: 4.078A pdb=" N ARG E 49 " --> pdb=" O ILE E 338 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 331 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 317 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA E 73 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET E 61 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 71 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TRP E 63 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 69 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 105 removed outlier: 6.240A pdb=" N CYS E 121 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU E 138 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE E 123 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 134 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 146 through 153 removed outlier: 6.448A pdb=" N GLN E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 161 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 178 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.686A pdb=" N SER E 189 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.783A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.457A pdb=" N GLY E 288 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL E 276 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 286 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 294 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL E 307 " --> pdb=" O CYS E 294 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 296 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.908A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1179 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: 2.48 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1457 1.30 - 1.43: 2440 1.43 - 1.56: 5240 1.56 - 1.69: 3 1.69 - 1.82: 101 Bond restraints: 9241 Sorted by residual: bond pdb=" C TYR A 261 " pdb=" O TYR A 261 " ideal model delta sigma weight residual 1.236 1.166 0.070 1.28e-02 6.10e+03 2.97e+01 bond pdb=" CA ARG A 208 " pdb=" C ARG A 208 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.28e-02 6.10e+03 2.73e+01 bond pdb=" C ARG A 208 " pdb=" O ARG A 208 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.22e-02 6.72e+03 2.29e+01 bond pdb=" C5 S12 A 401 " pdb=" O52 S12 A 401 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" NE ARG A 208 " pdb=" CZ ARG A 208 " ideal model delta sigma weight residual 1.326 1.302 0.024 1.10e-02 8.26e+03 4.73e+00 ... (remaining 9236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12389 2.48 - 4.96: 74 4.96 - 7.44: 14 7.44 - 9.93: 3 9.93 - 12.41: 2 Bond angle restraints: 12482 Sorted by residual: angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.09e+01 angle pdb=" C TYR A 261 " pdb=" N ALA A 262 " pdb=" CA ALA A 262 " ideal model delta sigma weight residual 120.29 127.73 -7.44 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N TYR A 261 " ideal model delta sigma weight residual 118.43 112.44 5.99 1.33e+00 5.65e-01 2.03e+01 angle pdb=" O LYS A 260 " pdb=" C LYS A 260 " pdb=" N TYR A 261 " ideal model delta sigma weight residual 122.46 128.46 -6.00 1.38e+00 5.25e-01 1.89e+01 angle pdb=" O3 S12 A 401 " pdb=" P S12 A 401 " pdb=" O4 S12 A 401 " ideal model delta sigma weight residual 121.84 109.43 12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 12477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.84: 5285 28.84 - 57.68: 204 57.68 - 86.51: 12 86.51 - 115.35: 0 115.35 - 144.19: 1 Dihedral angle restraints: 5502 sinusoidal: 2174 harmonic: 3328 Sorted by residual: dihedral pdb=" CA ASN A 116 " pdb=" C ASN A 116 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C4 S12 A 401 " pdb=" C5 S12 A 401 " pdb=" O52 S12 A 401 " pdb=" C6 S12 A 401 " ideal model delta sinusoidal sigma weight residual 176.02 31.83 144.19 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" CA ARG A 208 " pdb=" C ARG A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1098 0.045 - 0.091: 252 0.091 - 0.136: 63 0.136 - 0.182: 0 0.182 - 0.227: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE E 93 " pdb=" N ILE E 93 " pdb=" C ILE E 93 " pdb=" CB ILE E 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE S 216 " pdb=" N ILE S 216 " pdb=" C ILE S 216 " pdb=" CB ILE S 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1411 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO S 75 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 208 " 0.018 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG A 208 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG A 208 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 209 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 323 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 324 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.031 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 549 2.74 - 3.28: 8577 3.28 - 3.82: 13942 3.82 - 4.36: 16204 4.36 - 4.90: 29563 Nonbonded interactions: 68835 Sorted by model distance: nonbonded pdb=" OG SER E 245 " pdb=" OD1 ASP E 247 " model vdw 2.199 3.040 nonbonded pdb=" OG SER E 74 " pdb=" OD1 ASP E 76 " model vdw 2.206 3.040 nonbonded pdb=" NH1 ARG S 202 " pdb=" OE1 GLU S 220 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN A 200 " pdb=" OG1 THR A 202 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR E 274 " pdb=" O VAL E 315 " model vdw 2.280 3.040 ... (remaining 68830 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9241 Z= 0.183 Angle : 0.567 12.408 12482 Z= 0.321 Chirality : 0.039 0.227 1414 Planarity : 0.004 0.122 1566 Dihedral : 13.992 144.191 3352 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1133 helix: 2.30 (0.28), residues: 379 sheet: 1.13 (0.31), residues: 294 loop : -1.14 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 339 HIS 0.003 0.000 HIS S 35 PHE 0.015 0.001 PHE A 279 TYR 0.020 0.001 TYR A 261 ARG 0.006 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.023 Fit side-chains REVERT: A 74 ILE cc_start: 0.8371 (mm) cc_final: 0.8064 (mt) REVERT: D 345 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7941 (mttp) REVERT: E 153 ASP cc_start: 0.7447 (p0) cc_final: 0.7197 (p0) REVERT: S 154 SER cc_start: 0.7473 (m) cc_final: 0.7043 (p) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.2391 time to fit residues: 53.2099 Evaluate side-chains 130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 0.0670 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 206 HIS A 211 HIS D 255 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094536 restraints weight = 16342.331| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.24 r_work: 0.3152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9241 Z= 0.181 Angle : 0.523 6.504 12482 Z= 0.279 Chirality : 0.041 0.166 1414 Planarity : 0.004 0.073 1566 Dihedral : 6.245 100.748 1263 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 5.94 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.95 (0.26), residues: 1133 helix: 2.33 (0.27), residues: 394 sheet: 1.10 (0.31), residues: 292 loop : -1.34 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 339 HIS 0.006 0.001 HIS S 35 PHE 0.021 0.002 PHE A 205 TYR 0.024 0.002 TYR A 77 ARG 0.005 0.000 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.896 Fit side-chains REVERT: A 279 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.4118 (t80) REVERT: C 58 GLU cc_start: 0.7297 (mp0) cc_final: 0.7057 (mp0) REVERT: D 248 LYS cc_start: 0.8747 (tttt) cc_final: 0.8127 (mmtt) REVERT: D 347 ASN cc_start: 0.8056 (t0) cc_final: 0.7806 (t0) REVERT: E 258 ASP cc_start: 0.6914 (t0) cc_final: 0.6472 (t0) REVERT: S 154 SER cc_start: 0.7423 (m) cc_final: 0.7024 (p) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.2486 time to fit residues: 44.6805 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087969 restraints weight = 16748.007| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.17 r_work: 0.3037 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9241 Z= 0.371 Angle : 0.642 9.082 12482 Z= 0.343 Chirality : 0.045 0.175 1414 Planarity : 0.005 0.064 1566 Dihedral : 5.829 92.100 1261 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.71 % Allowed : 9.66 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.50 (0.25), residues: 1133 helix: 2.14 (0.27), residues: 387 sheet: 0.78 (0.30), residues: 286 loop : -1.64 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 339 HIS 0.006 0.002 HIS S 35 PHE 0.021 0.002 PHE A 205 TYR 0.027 0.002 TYR E 105 ARG 0.007 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.057 Fit side-chains REVERT: A 105 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: A 158 ARG cc_start: 0.4400 (tpm170) cc_final: 0.3876 (ttt180) REVERT: A 325 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7588 (t) REVERT: D 248 LYS cc_start: 0.8809 (tttt) cc_final: 0.8293 (mmtt) REVERT: D 275 GLU cc_start: 0.8021 (tp30) cc_final: 0.7781 (tm-30) REVERT: D 318 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: D 347 ASN cc_start: 0.8247 (t0) cc_final: 0.7890 (t0) REVERT: E 258 ASP cc_start: 0.7061 (t0) cc_final: 0.6857 (t0) REVERT: S 154 SER cc_start: 0.7508 (m) cc_final: 0.7045 (t) outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 0.2415 time to fit residues: 46.4218 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088857 restraints weight = 16606.304| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.14 r_work: 0.3052 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9241 Z= 0.275 Angle : 0.564 7.767 12482 Z= 0.303 Chirality : 0.043 0.180 1414 Planarity : 0.004 0.056 1566 Dihedral : 5.624 73.593 1261 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.91 % Allowed : 12.27 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.51 (0.25), residues: 1133 helix: 2.29 (0.27), residues: 387 sheet: 0.70 (0.30), residues: 279 loop : -1.68 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 47 HIS 0.005 0.001 HIS D 213 PHE 0.022 0.002 PHE A 205 TYR 0.020 0.002 TYR A 77 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.983 Fit side-chains REVERT: A 158 ARG cc_start: 0.4514 (tpm170) cc_final: 0.3987 (ttm170) REVERT: A 189 MET cc_start: 0.6789 (tpp) cc_final: 0.6520 (tpp) REVERT: A 245 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7327 (mp) REVERT: A 325 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (t) REVERT: D 248 LYS cc_start: 0.8791 (tttt) cc_final: 0.8290 (mmtt) REVERT: D 347 ASN cc_start: 0.8295 (t0) cc_final: 0.7770 (t0) REVERT: E 258 ASP cc_start: 0.7097 (t0) cc_final: 0.6890 (t0) REVERT: S 154 SER cc_start: 0.7589 (m) cc_final: 0.7108 (t) outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 0.2494 time to fit residues: 46.7878 Evaluate side-chains 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 0.0270 chunk 100 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.091722 restraints weight = 16575.890| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.13 r_work: 0.3107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9241 Z= 0.151 Angle : 0.483 8.449 12482 Z= 0.261 Chirality : 0.041 0.194 1414 Planarity : 0.004 0.051 1566 Dihedral : 5.105 57.517 1261 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.91 % Allowed : 13.08 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.25), residues: 1133 helix: 2.40 (0.27), residues: 394 sheet: 0.77 (0.30), residues: 285 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS D 213 PHE 0.023 0.001 PHE A 205 TYR 0.018 0.001 TYR A 77 ARG 0.005 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.027 Fit side-chains REVERT: A 105 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: A 158 ARG cc_start: 0.4405 (tpm170) cc_final: 0.3892 (ttm170) REVERT: D 248 LYS cc_start: 0.8778 (tttt) cc_final: 0.8250 (mmtt) REVERT: D 275 GLU cc_start: 0.7981 (tp30) cc_final: 0.7763 (tm-30) REVERT: D 347 ASN cc_start: 0.8292 (t0) cc_final: 0.7744 (t0) REVERT: E 258 ASP cc_start: 0.7079 (t0) cc_final: 0.6878 (t0) REVERT: S 140 MET cc_start: 0.8548 (mmm) cc_final: 0.7342 (mmt) REVERT: S 154 SER cc_start: 0.7525 (m) cc_final: 0.7068 (t) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.2429 time to fit residues: 45.8937 Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 347 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 = 0.3652 r_free = 0.3652 target = 0.114855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089368 restraints weight = 16634.142| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.13 r_work: 0.3065 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9241 Z= 0.228 Angle : 0.528 7.751 12482 Z= 0.283 Chirality : 0.042 0.198 1414 Planarity : 0.004 0.045 1566 Dihedral : 5.097 54.929 1261 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.52 % Allowed : 13.18 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.63 (0.25), residues: 1133 helix: 2.39 (0.27), residues: 393 sheet: 0.69 (0.30), residues: 284 loop : -1.62 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.002 PHE A 205 TYR 0.016 0.002 TYR S 95 ARG 0.005 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.055 Fit side-chains REVERT: A 105 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8156 (m-10) REVERT: A 158 ARG cc_start: 0.4427 (tpm170) cc_final: 0.3957 (ttm170) REVERT: A 189 MET cc_start: 0.6765 (tpp) cc_final: 0.6493 (tpp) REVERT: A 245 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6898 (mp) REVERT: D 248 LYS cc_start: 0.8771 (tttt) cc_final: 0.8235 (mmtt) REVERT: D 347 ASN cc_start: 0.8351 (t0) cc_final: 0.7730 (t0) REVERT: E 258 ASP cc_start: 0.7040 (t0) cc_final: 0.6831 (t0) REVERT: S 154 SER cc_start: 0.7570 (m) cc_final: 0.7120 (t) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.2311 time to fit residues: 45.5931 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 347 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 = 0.3667 r_free = 0.3667 target = 0.115919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090296 restraints weight = 16792.131| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.19 r_work: 0.3082 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9241 Z= 0.174 Angle : 0.496 7.772 12482 Z= 0.267 Chirality : 0.041 0.203 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.998 55.917 1261 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.11 % Allowed : 14.39 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.68 (0.25), residues: 1133 helix: 2.44 (0.27), residues: 394 sheet: 0.66 (0.30), residues: 286 loop : -1.58 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS D 213 PHE 0.025 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.458 Fit side-chains REVERT: A 105 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: A 158 ARG cc_start: 0.4402 (tpm170) cc_final: 0.3903 (ttm170) REVERT: A 245 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6725 (mp) REVERT: D 248 LYS cc_start: 0.8719 (tttt) cc_final: 0.8168 (mmtt) REVERT: D 275 GLU cc_start: 0.8055 (tp30) cc_final: 0.7768 (tm-30) REVERT: D 347 ASN cc_start: 0.8330 (t0) cc_final: 0.7746 (t0) REVERT: E 258 ASP cc_start: 0.7010 (t0) cc_final: 0.6797 (t0) REVERT: S 154 SER cc_start: 0.7507 (m) cc_final: 0.7061 (t) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.2906 time to fit residues: 57.2186 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092569 restraints weight = 16821.200| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.19 r_work: 0.3123 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9241 Z= 0.133 Angle : 0.469 8.192 12482 Z= 0.252 Chirality : 0.040 0.212 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.865 57.508 1261 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.91 % Allowed : 14.69 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.85 (0.25), residues: 1133 helix: 2.58 (0.27), residues: 392 sheet: 0.85 (0.30), residues: 285 loop : -1.54 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.002 0.001 HIS D 213 PHE 0.025 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: A 158 ARG cc_start: 0.4435 (tpm170) cc_final: 0.3880 (ttm170) REVERT: A 206 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.6613 (t-90) REVERT: D 248 LYS cc_start: 0.8724 (tttt) cc_final: 0.8163 (mmtt) REVERT: D 275 GLU cc_start: 0.8012 (tp30) cc_final: 0.7810 (tm-30) REVERT: D 347 ASN cc_start: 0.8328 (t0) cc_final: 0.7767 (t0) REVERT: E 258 ASP cc_start: 0.7029 (t0) cc_final: 0.6817 (t0) REVERT: S 154 SER cc_start: 0.7454 (m) cc_final: 0.6832 (t) REVERT: S 155 VAL cc_start: 0.8119 (t) cc_final: 0.7505 (p) outliers start: 19 outliers final: 17 residues processed: 146 average time/residue: 0.2350 time to fit residues: 46.6473 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092483 restraints weight = 16456.903| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.14 r_work: 0.3124 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9241 Z= 0.143 Angle : 0.485 7.336 12482 Z= 0.261 Chirality : 0.041 0.246 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.850 57.034 1261 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.01 % Allowed : 14.49 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.88 (0.25), residues: 1133 helix: 2.59 (0.27), residues: 392 sheet: 0.84 (0.30), residues: 292 loop : -1.52 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS D 213 PHE 0.026 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.005 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: A 158 ARG cc_start: 0.4566 (tpm170) cc_final: 0.4040 (ttm170) REVERT: A 206 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.6642 (t-90) REVERT: A 245 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6564 (mp) REVERT: D 240 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.5052 (tmm) REVERT: D 248 LYS cc_start: 0.8839 (tttt) cc_final: 0.8333 (mmtt) REVERT: D 318 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: D 347 ASN cc_start: 0.8337 (t0) cc_final: 0.7780 (t0) REVERT: S 154 SER cc_start: 0.7509 (m) cc_final: 0.6887 (t) REVERT: S 155 VAL cc_start: 0.8212 (t) cc_final: 0.7620 (p) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.2365 time to fit residues: 44.1078 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.1980 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092101 restraints weight = 16639.206| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.14 r_work: 0.3119 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9241 Z= 0.155 Angle : 0.500 8.436 12482 Z= 0.270 Chirality : 0.041 0.291 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.874 56.791 1261 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.01 % Allowed : 15.09 % Favored : 82.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.00 % 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: 0.84 (0.25), residues: 1133 helix: 2.57 (0.27), residues: 393 sheet: 0.78 (0.30), residues: 294 loop : -1.55 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS D 213 PHE 0.025 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.005 0.000 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.988 Fit side-chains REVERT: A 158 ARG cc_start: 0.4536 (tpm170) cc_final: 0.4007 (ttm170) REVERT: A 206 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6688 (t-90) REVERT: A 245 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6554 (mp) REVERT: D 240 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5039 (tmm) REVERT: D 248 LYS cc_start: 0.8779 (tttt) cc_final: 0.8243 (mmtt) REVERT: D 318 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: D 347 ASN cc_start: 0.8337 (t0) cc_final: 0.7756 (t0) REVERT: E 262 MET cc_start: 0.8595 (mtp) cc_final: 0.8372 (ttm) REVERT: S 154 SER cc_start: 0.7491 (m) cc_final: 0.7051 (t) outliers start: 20 outliers final: 15 residues processed: 135 average time/residue: 0.2760 time to fit residues: 50.9393 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 347 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 = 0.3667 r_free = 0.3667 target = 0.115785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090366 restraints weight = 16515.358| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.12 r_work: 0.3084 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9241 Z= 0.215 Angle : 0.541 9.245 12482 Z= 0.289 Chirality : 0.042 0.292 1414 Planarity : 0.004 0.045 1566 Dihedral : 5.007 56.825 1261 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.91 % Allowed : 15.39 % Favored : 82.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.00 % 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: 0.74 (0.25), residues: 1133 helix: 2.51 (0.27), residues: 393 sheet: 0.74 (0.30), residues: 289 loop : -1.61 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS D 213 PHE 0.027 0.002 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.005 0.000 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.30 seconds wall clock time: 98 minutes 44.21 seconds (5924.21 seconds total)