Starting phenix.real_space_refine on Mon May 12 17:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sai_40270/05_2025/8sai_40270_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sai_40270/05_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_40270/05_2025/8sai_40270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sai_40270/05_2025/8sai_40270.map" model { file = "/net/cci-nas-00/data/ceres_data/8sai_40270/05_2025/8sai_40270_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sai_40270/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.17, per 1000 atoms: 0.68 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.06 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: 2.73 Time building geometry restraints manager: 2.73 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: 0.010 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.090 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- 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 9243 Z= 0.162 Angle : 0.567 12.408 12486 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 Details of bonding type rmsd hydrogen bonds : bond 0.15386 ( 417) hydrogen bonds : angle 4.91679 ( 1179) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.90840 ( 4) covalent geometry : bond 0.00281 ( 9241) covalent geometry : angle 0.56666 (12482) *********************** 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 : 1.025 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: 0.2407 time to fit residues: 53.2354 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 : 1.056 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094525 restraints weight = 16342.334| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.24 r_work: 0.3152 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.50 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 9243 Z= 0.128 Angle : 0.523 6.504 12486 Z= 0.280 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 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 417) hydrogen bonds : angle 3.96530 ( 1179) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.14020 ( 4) covalent geometry : bond 0.00288 ( 9241) covalent geometry : angle 0.52267 (12482) *********************** 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 : 1.030 Fit side-chains REVERT: A 279 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.4117 (t80) REVERT: C 58 GLU cc_start: 0.7296 (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: 0.7807 (t0) REVERT: E 258 ASP cc_start: 0.6910 (t0) cc_final: 0.6469 (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: 0.2563 time to fit residues: 46.1556 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 : 0.971 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.113331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087433 restraints weight = 16777.067| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.18 r_work: 0.3023 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9243 Z= 0.280 Angle : 0.675 9.873 12486 Z= 0.360 Chirality : 0.046 0.171 1414 Planarity : 0.005 0.064 1566 Dihedral : 5.980 96.177 1261 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.81 % Allowed : 9.36 % Favored : 88.83 % 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: 0.42 (0.25), residues: 1133 helix: 1.99 (0.26), residues: 391 sheet: 0.78 (0.30), residues: 285 loop : -1.66 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 339 HIS 0.007 0.002 HIS S 35 PHE 0.022 0.003 PHE A 205 TYR 0.029 0.003 TYR E 105 ARG 0.005 0.001 ARG S 202 Details of bonding type rmsd hydrogen bonds : bond 0.06477 ( 417) hydrogen bonds : angle 4.41594 ( 1179) SS BOND : bond 0.00931 ( 2) SS BOND : angle 1.50640 ( 4) covalent geometry : bond 0.00689 ( 9241) covalent geometry : angle 0.67409 (12482) *********************** 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 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.995 Fit side-chains REVERT: A 105 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: A 158 ARG cc_start: 0.4317 (tpm170) cc_final: 0.3663 (ttt180) REVERT: A 325 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (t) REVERT: D 248 LYS cc_start: 0.8816 (tttt) cc_final: 0.8292 (mmtt) REVERT: D 275 GLU cc_start: 0.8033 (tp30) cc_final: 0.7820 (tm-30) REVERT: D 318 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: D 347 ASN cc_start: 0.8268 (t0) cc_final: 0.7899 (t0) REVERT: S 154 SER cc_start: 0.7496 (m) cc_final: 0.7026 (t) outliers start: 18 outliers final: 11 residues processed: 143 average time/residue: 0.2427 time to fit residues: 46.5891 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 : 0.970 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.115765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090175 restraints weight = 16572.968| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.14 r_work: 0.3078 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9243 Z= 0.135 Angle : 0.521 7.470 12486 Z= 0.281 Chirality : 0.041 0.175 1414 Planarity : 0.004 0.055 1566 Dihedral : 5.540 77.598 1261 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.01 % Allowed : 11.67 % Favored : 86.32 % 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: 0.65 (0.25), residues: 1133 helix: 2.38 (0.27), residues: 387 sheet: 0.79 (0.30), residues: 285 loop : -1.60 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS D 213 PHE 0.023 0.002 PHE A 205 TYR 0.020 0.001 TYR A 77 ARG 0.003 0.000 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 417) hydrogen bonds : angle 4.03678 ( 1179) SS BOND : bond 0.00590 ( 2) SS BOND : angle 1.21943 ( 4) covalent geometry : bond 0.00308 ( 9241) covalent geometry : angle 0.52048 (12482) *********************** 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 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.011 Fit side-chains REVERT: A 158 ARG cc_start: 0.4405 (tpm170) cc_final: 0.3770 (ttm170) REVERT: A 245 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7205 (mp) REVERT: D 248 LYS cc_start: 0.8779 (tttt) cc_final: 0.8275 (mmtt) REVERT: D 347 ASN cc_start: 0.8237 (t0) cc_final: 0.7733 (t0) REVERT: S 154 SER cc_start: 0.7549 (m) cc_final: 0.7058 (t) outliers start: 20 outliers final: 18 residues processed: 136 average time/residue: 0.2388 time to fit residues: 43.7075 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 : 1.096 ------------------------------------------------------------------------------- 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 334 ILE 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 192 MET 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: 0.3980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.116266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090703 restraints weight = 16582.072| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.14 r_work: 0.3084 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.130 Angle : 0.507 8.527 12486 Z= 0.273 Chirality : 0.041 0.193 1414 Planarity : 0.003 0.044 1566 Dihedral : 5.199 56.940 1261 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.21 % Allowed : 12.68 % Favored : 85.11 % 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: 0.69 (0.25), residues: 1133 helix: 2.36 (0.27), residues: 394 sheet: 0.79 (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 0.004 0.001 HIS D 213 PHE 0.022 0.001 PHE A 205 TYR 0.019 0.001 TYR A 77 ARG 0.005 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 417) hydrogen bonds : angle 3.92390 ( 1179) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.21242 ( 4) covalent geometry : bond 0.00298 ( 9241) covalent geometry : angle 0.50698 (12482) *********************** 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 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.003 Fit side-chains REVERT: A 105 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: A 158 ARG cc_start: 0.4479 (tpm170) cc_final: 0.3911 (ttm170) REVERT: A 189 MET cc_start: 0.6794 (tpp) cc_final: 0.6505 (tpp) REVERT: A 245 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.6926 (mp) REVERT: A 251 ARG cc_start: 0.8943 (tmm-80) cc_final: 0.8736 (tmm-80) REVERT: D 248 LYS cc_start: 0.8788 (tttt) cc_final: 0.8262 (mmtt) REVERT: D 275 GLU cc_start: 0.8018 (tp30) cc_final: 0.7762 (tm-30) REVERT: D 347 ASN cc_start: 0.8327 (t0) cc_final: 0.7765 (t0) REVERT: S 140 MET cc_start: 0.8581 (mmm) cc_final: 0.7439 (mmt) REVERT: S 154 SER cc_start: 0.7512 (m) cc_final: 0.7042 (t) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.2360 time to fit residues: 45.2394 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 321 THR 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 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=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: 1.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 206 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090909 restraints weight = 16590.838| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.14 r_work: 0.3092 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.122 Angle : 0.498 8.770 12486 Z= 0.266 Chirality : 0.041 0.203 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.991 56.009 1261 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 13.38 % Favored : 84.10 % 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: 0.73 (0.25), residues: 1133 helix: 2.41 (0.27), residues: 394 sheet: 0.78 (0.30), residues: 284 loop : -1.55 (0.26), residues: 455 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 0.024 0.001 PHE A 205 TYR 0.016 0.001 TYR A 77 ARG 0.002 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 417) hydrogen bonds : angle 3.83153 ( 1179) SS BOND : bond 0.00516 ( 2) SS BOND : angle 1.12245 ( 4) covalent geometry : bond 0.00279 ( 9241) covalent geometry : angle 0.49733 (12482) *********************** 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 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.965 Fit side-chains REVERT: A 105 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8135 (m-10) REVERT: A 158 ARG cc_start: 0.4542 (tpm170) cc_final: 0.4016 (ttm170) REVERT: A 245 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6812 (mp) REVERT: D 248 LYS cc_start: 0.8786 (tttt) cc_final: 0.8256 (mmtt) REVERT: D 347 ASN cc_start: 0.8347 (t0) cc_final: 0.7771 (t0) REVERT: S 154 SER cc_start: 0.7514 (m) cc_final: 0.7059 (t) outliers start: 25 outliers final: 18 residues processed: 142 average time/residue: 0.2344 time to fit residues: 44.7033 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 D residue 253 ILE 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 270 ILE 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 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.0270 chunk 111 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.117855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092326 restraints weight = 16747.747| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.16 r_work: 0.3119 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9243 Z= 0.101 Angle : 0.472 7.914 12486 Z= 0.254 Chirality : 0.040 0.208 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.848 57.059 1261 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.51 % Allowed : 14.69 % Favored : 83.80 % 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: 0.84 (0.25), residues: 1133 helix: 2.55 (0.27), residues: 392 sheet: 0.86 (0.30), residues: 283 loop : -1.53 (0.26), residues: 458 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 0.024 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 417) hydrogen bonds : angle 3.67215 ( 1179) SS BOND : bond 0.00416 ( 2) SS BOND : angle 1.06371 ( 4) covalent geometry : bond 0.00220 ( 9241) covalent geometry : angle 0.47215 (12482) *********************** 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 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: A 158 ARG cc_start: 0.4559 (tpm170) cc_final: 0.4064 (ttm170) REVERT: A 245 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6667 (mp) REVERT: D 240 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.5117 (tmm) REVERT: D 248 LYS cc_start: 0.8832 (tttt) cc_final: 0.8319 (mmtt) REVERT: D 275 GLU cc_start: 0.8018 (tp30) cc_final: 0.7801 (tm-30) REVERT: D 347 ASN cc_start: 0.8360 (t0) cc_final: 0.7798 (t0) REVERT: S 154 SER cc_start: 0.7519 (m) cc_final: 0.7074 (t) outliers start: 15 outliers final: 10 residues processed: 135 average time/residue: 0.2284 time to fit residues: 41.6819 Evaluate side-chains 133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain D residue 240 MET 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 234 PHE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.117143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.091434 restraints weight = 16831.712| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.19 r_work: 0.3105 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.114 Angle : 0.500 11.280 12486 Z= 0.266 Chirality : 0.041 0.207 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.856 56.113 1261 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 2.55 (0.27), residues: 393 sheet: 0.91 (0.30), residues: 285 loop : -1.56 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.025 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 417) hydrogen bonds : angle 3.68215 ( 1179) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.08469 ( 4) covalent geometry : bond 0.00257 ( 9241) covalent geometry : angle 0.49997 (12482) *********************** 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 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: A 158 ARG cc_start: 0.4510 (tpm170) cc_final: 0.3945 (ttm170) REVERT: A 189 MET cc_start: 0.6480 (tpp) cc_final: 0.6253 (tpt) REVERT: A 245 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6667 (mp) REVERT: D 240 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5155 (tmm) REVERT: D 248 LYS cc_start: 0.8742 (tttt) cc_final: 0.8188 (mmtt) REVERT: D 275 GLU cc_start: 0.8006 (tp30) cc_final: 0.7788 (tm-30) REVERT: D 347 ASN cc_start: 0.8367 (t0) cc_final: 0.7750 (t0) REVERT: S 154 SER cc_start: 0.7455 (m) cc_final: 0.7012 (t) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.2502 time to fit residues: 46.8267 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 240 MET 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 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 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: 0.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091450 restraints weight = 16487.674| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.17 r_work: 0.3104 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9243 Z= 0.115 Angle : 0.502 10.126 12486 Z= 0.266 Chirality : 0.041 0.207 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.881 55.671 1261 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.01 % Allowed : 14.39 % Favored : 83.60 % 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: 0.87 (0.25), residues: 1133 helix: 2.57 (0.27), residues: 393 sheet: 0.90 (0.30), residues: 292 loop : -1.57 (0.26), residues: 448 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 0.026 0.001 PHE A 205 TYR 0.016 0.001 TYR A 77 ARG 0.006 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 417) hydrogen bonds : angle 3.67532 ( 1179) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.01936 ( 4) covalent geometry : bond 0.00260 ( 9241) covalent geometry : angle 0.50126 (12482) *********************** 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 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: A 158 ARG cc_start: 0.4514 (tpm170) cc_final: 0.3962 (ttm170) REVERT: A 245 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6592 (mp) REVERT: D 240 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.5149 (tmm) REVERT: D 248 LYS cc_start: 0.8740 (tttt) cc_final: 0.8186 (mmtt) REVERT: D 347 ASN cc_start: 0.8355 (t0) cc_final: 0.7746 (t0) REVERT: S 154 SER cc_start: 0.7456 (m) cc_final: 0.7013 (t) outliers start: 20 outliers final: 17 residues processed: 139 average time/residue: 0.2382 time to fit residues: 44.8544 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 240 MET 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 270 ILE 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 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: 0.6980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.117998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092611 restraints weight = 16683.981| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.14 r_work: 0.3126 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.002 0.031 9243 Z= 0.103 Angle : 0.484 7.222 12486 Z= 0.261 Chirality : 0.041 0.266 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.922 56.555 1261 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.61 % Allowed : 15.09 % Favored : 83.30 % 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 (0.25), residues: 1133 helix: 2.64 (0.27), residues: 393 sheet: 0.93 (0.30), residues: 292 loop : -1.53 (0.27), residues: 448 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 0.027 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.005 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 417) hydrogen bonds : angle 3.59438 ( 1179) SS BOND : bond 0.00408 ( 2) SS BOND : angle 0.96227 ( 4) covalent geometry : bond 0.00221 ( 9241) covalent geometry : angle 0.48384 (12482) ********************** 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 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.4572 (tpm170) cc_final: 0.4040 (ttm170) REVERT: A 245 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6512 (mp) REVERT: D 240 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5132 (tmm) REVERT: D 248 LYS cc_start: 0.8766 (tttt) cc_final: 0.8230 (mmtt) REVERT: D 347 ASN cc_start: 0.8342 (t0) cc_final: 0.7768 (t0) REVERT: S 154 SER cc_start: 0.7476 (m) cc_final: 0.7037 (t) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.2286 time to fit residues: 41.3903 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 245 LEU 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 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 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.114298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088734 restraints weight = 16576.098| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.13 r_work: 0.3053 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9243 Z= 0.183 Angle : 0.581 8.568 12486 Z= 0.311 Chirality : 0.044 0.268 1414 Planarity : 0.004 0.046 1566 Dihedral : 5.277 57.682 1261 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.01 % Allowed : 15.39 % Favored : 82.60 % 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: 0.71 (0.25), residues: 1133 helix: 2.47 (0.26), residues: 393 sheet: 0.79 (0.30), residues: 288 loop : -1.66 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 339 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.002 PHE A 205 TYR 0.018 0.002 TYR S 95 ARG 0.005 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 417) hydrogen bonds : angle 3.95510 ( 1179) SS BOND : bond 0.00654 ( 2) SS BOND : angle 1.13715 ( 4) covalent geometry : bond 0.00440 ( 9241) covalent geometry : angle 0.58098 (12482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4988.77 seconds wall clock time: 87 minutes 2.11 seconds (5222.11 seconds total)