Starting phenix.real_space_refine on Wed Apr 30 04:12:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sai_40270/04_2025/8sai_40270_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sai_40270/04_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_40270/04_2025/8sai_40270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sai_40270/04_2025/8sai_40270.map" model { file = "/net/cci-nas-00/data/ceres_data/8sai_40270/04_2025/8sai_40270_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sai_40270/04_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-5669/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: 5.41, per 1000 atoms: 0.60 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: 2.17 Conformation dependent library (CDL) restraints added in 986.5 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: 0.92 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: 2.40 Time building geometry restraints manager: 2.55 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: 0.880 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.420 Find NCS groups from input model: 0.120 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- 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 : 1.438 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: 0.2469 time to fit residues: 55.0256 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 : 0.911 ------------------------------------------------------------------------------- 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 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 : 1.502 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: 0.3110 time to fit residues: 56.3657 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 : 1.380 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.8980 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.114543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088503 restraints weight = 16752.815| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.17 r_work: 0.3076 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9243 Z= 0.238 Angle : 0.632 9.228 12486 Z= 0.336 Chirality : 0.045 0.179 1414 Planarity : 0.005 0.064 1566 Dihedral : 5.847 95.708 1261 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.51 % Allowed : 9.96 % Favored : 88.53 % 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: 2.10 (0.26), residues: 392 sheet: 0.80 (0.30), residues: 281 loop : -1.61 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 339 HIS 0.006 0.002 HIS E 142 PHE 0.022 0.002 PHE A 205 TYR 0.026 0.002 TYR E 105 ARG 0.004 0.001 ARG E 314 Details of bonding type rmsd hydrogen bonds : bond 0.05912 ( 417) hydrogen bonds : angle 4.25717 ( 1179) SS BOND : bond 0.00789 ( 2) SS BOND : angle 1.24676 ( 4) covalent geometry : bond 0.00579 ( 9241) covalent geometry : angle 0.63147 (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 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.947 Fit side-chains REVERT: A 158 ARG cc_start: 0.4534 (tpm170) cc_final: 0.3661 (ttt180) REVERT: D 248 LYS cc_start: 0.8872 (tttt) cc_final: 0.8359 (mmtt) REVERT: D 275 GLU cc_start: 0.8015 (tp30) cc_final: 0.7811 (tm-30) REVERT: D 347 ASN cc_start: 0.8255 (t0) cc_final: 0.7892 (t0) REVERT: S 154 SER cc_start: 0.7597 (m) cc_final: 0.7152 (t) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.2404 time to fit residues: 45.9339 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 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 E residue 37 ILE 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: 0.9980 chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.115961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090194 restraints weight = 16518.696| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.15 r_work: 0.3076 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9243 Z= 0.150 Angle : 0.530 7.225 12486 Z= 0.286 Chirality : 0.042 0.176 1414 Planarity : 0.004 0.057 1566 Dihedral : 5.481 78.436 1261 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.91 % Allowed : 11.27 % Favored : 86.82 % 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: 0.59 (0.25), residues: 1133 helix: 2.27 (0.27), residues: 393 sheet: 0.73 (0.30), residues: 286 loop : -1.62 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS D 213 PHE 0.021 0.002 PHE A 205 TYR 0.022 0.002 TYR A 77 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 417) hydrogen bonds : angle 4.01684 ( 1179) SS BOND : bond 0.00639 ( 2) SS BOND : angle 1.23100 ( 4) covalent geometry : bond 0.00352 ( 9241) covalent geometry : angle 0.52996 (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 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.099 Fit side-chains REVERT: A 105 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: A 158 ARG cc_start: 0.4293 (tpm170) cc_final: 0.3574 (ttm170) REVERT: A 245 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7189 (mp) REVERT: D 248 LYS cc_start: 0.8781 (tttt) cc_final: 0.8277 (mmtt) REVERT: D 318 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: D 347 ASN cc_start: 0.8258 (t0) cc_final: 0.7754 (t0) REVERT: S 154 SER cc_start: 0.7549 (m) cc_final: 0.7088 (t) outliers start: 19 outliers final: 16 residues processed: 139 average time/residue: 0.2375 time to fit residues: 44.6897 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 : 0.952 ------------------------------------------------------------------------------- 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 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 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 318 GLU 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 158 SER 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: 0.7980 chunk 69 optimal weight: 1.9990 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: 0.9990 chunk 85 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.117096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.091495 restraints weight = 16480.494| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.14 r_work: 0.3101 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2812 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= 0.117 Angle : 0.491 6.604 12486 Z= 0.266 Chirality : 0.041 0.196 1414 Planarity : 0.003 0.044 1566 Dihedral : 5.135 58.849 1261 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.01 % Allowed : 11.77 % Favored : 86.22 % 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: 0.72 (0.25), residues: 1133 helix: 2.41 (0.27), residues: 394 sheet: 0.79 (0.30), residues: 285 loop : -1.57 (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 0.021 0.001 PHE A 205 TYR 0.020 0.001 TYR A 77 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 417) hydrogen bonds : angle 3.84050 ( 1179) SS BOND : bond 0.00510 ( 2) SS BOND : angle 1.11373 ( 4) covalent geometry : bond 0.00263 ( 9241) covalent geometry : angle 0.49068 (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 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.028 Fit side-chains REVERT: A 105 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: A 158 ARG cc_start: 0.4331 (tpm170) cc_final: 0.3683 (ttm170) REVERT: D 248 LYS cc_start: 0.8774 (tttt) cc_final: 0.8240 (mmtt) REVERT: D 275 GLU cc_start: 0.7943 (tp30) cc_final: 0.7718 (tm-30) REVERT: D 347 ASN cc_start: 0.8300 (t0) cc_final: 0.7750 (t0) REVERT: S 140 MET cc_start: 0.8544 (mmm) cc_final: 0.7343 (mmt) REVERT: S 154 SER cc_start: 0.7446 (m) cc_final: 0.6979 (t) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 0.2377 time to fit residues: 44.9702 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 190 ILE Chi-restraints excluded: chain A residue 334 ILE 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 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 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: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3672 r_free = 0.3672 target = 0.116196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090527 restraints weight = 16524.196| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.15 r_work: 0.3084 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9243 Z= 0.131 Angle : 0.513 8.957 12486 Z= 0.274 Chirality : 0.041 0.197 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.996 56.511 1261 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.62 % Allowed : 11.97 % Favored : 85.41 % 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: 2.39 (0.27), residues: 394 sheet: 0.75 (0.30), residues: 287 loop : -1.57 (0.26), residues: 452 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 0.021 0.001 PHE A 205 TYR 0.018 0.001 TYR A 77 ARG 0.005 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 417) hydrogen bonds : angle 3.87891 ( 1179) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.13141 ( 4) covalent geometry : bond 0.00305 ( 9241) covalent geometry : angle 0.51317 (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 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.961 Fit side-chains REVERT: A 105 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: A 158 ARG cc_start: 0.4447 (tpm170) cc_final: 0.3847 (ttm170) REVERT: A 189 MET cc_start: 0.6840 (tpp) cc_final: 0.6527 (tpp) REVERT: D 248 LYS cc_start: 0.8831 (tttt) cc_final: 0.8330 (mmtt) REVERT: D 318 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: D 347 ASN cc_start: 0.8350 (t0) cc_final: 0.7771 (t0) REVERT: S 154 SER cc_start: 0.7550 (m) cc_final: 0.7091 (t) outliers start: 26 outliers final: 20 residues processed: 141 average time/residue: 0.2362 time to fit residues: 45.2217 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 334 ILE Chi-restraints excluded: chain C residue 58 GLU 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 D residue 318 GLU 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 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: 0.9990 chunk 112 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 = 0.117176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091443 restraints weight = 16689.527| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.14 r_work: 0.3102 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2997 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= 0.113 Angle : 0.494 9.037 12486 Z= 0.264 Chirality : 0.041 0.208 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.903 56.487 1261 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.31 % Allowed : 12.88 % Favored : 84.81 % 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: 0.81 (0.25), residues: 1133 helix: 2.52 (0.27), residues: 391 sheet: 0.79 (0.30), residues: 287 loop : -1.50 (0.27), residues: 455 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 0.022 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.004 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 417) hydrogen bonds : angle 3.75941 ( 1179) SS BOND : bond 0.00469 ( 2) SS BOND : angle 1.05620 ( 4) covalent geometry : bond 0.00253 ( 9241) covalent geometry : angle 0.49371 (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 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: A 158 ARG cc_start: 0.4526 (tpm170) cc_final: 0.3970 (ttm170) REVERT: A 189 MET cc_start: 0.6843 (tpp) cc_final: 0.6573 (tpp) REVERT: D 248 LYS cc_start: 0.8837 (tttt) cc_final: 0.8331 (mmtt) REVERT: D 275 GLU cc_start: 0.8015 (tp30) cc_final: 0.7785 (tm-30) REVERT: D 318 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: D 347 ASN cc_start: 0.8348 (t0) cc_final: 0.7786 (t0) REVERT: S 154 SER cc_start: 0.7513 (m) cc_final: 0.7067 (t) outliers start: 23 outliers final: 19 residues processed: 138 average time/residue: 0.2434 time to fit residues: 44.9919 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 C residue 58 GLU 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 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 263 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL 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: 0.8980 chunk 11 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3699 r_free = 0.3699 target = 0.118102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092499 restraints weight = 16796.893| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.15 r_work: 0.3124 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9243 Z= 0.102 Angle : 0.474 6.995 12486 Z= 0.255 Chirality : 0.040 0.215 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.836 57.237 1261 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 13.38 % 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: 0.90 (0.25), residues: 1133 helix: 2.60 (0.27), residues: 391 sheet: 0.87 (0.31), residues: 285 loop : -1.46 (0.27), residues: 457 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 0.023 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.004 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 417) hydrogen bonds : angle 3.64496 ( 1179) SS BOND : bond 0.00420 ( 2) SS BOND : angle 1.00645 ( 4) covalent geometry : bond 0.00222 ( 9241) covalent geometry : angle 0.47350 (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 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.4530 (tpm170) cc_final: 0.3946 (ttm170) REVERT: A 279 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.4509 (t80) REVERT: D 248 LYS cc_start: 0.8764 (tttt) cc_final: 0.8220 (mmtt) REVERT: D 318 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: D 347 ASN cc_start: 0.8342 (t0) cc_final: 0.7759 (t0) REVERT: S 154 SER cc_start: 0.7498 (m) cc_final: 0.7054 (t) outliers start: 23 outliers final: 19 residues processed: 138 average time/residue: 0.2548 time to fit residues: 47.3119 Evaluate side-chains 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 112 MET 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 279 PHE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 262 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.117625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092117 restraints weight = 16441.965| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.12 r_work: 0.3117 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3062 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= 0.108 Angle : 0.482 7.470 12486 Z= 0.258 Chirality : 0.041 0.211 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.854 56.702 1261 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 13.48 % Favored : 84.00 % 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: 2.61 (0.27), residues: 391 sheet: 0.89 (0.30), residues: 287 loop : -1.54 (0.26), residues: 455 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 0.024 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.004 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 417) hydrogen bonds : angle 3.65153 ( 1179) SS BOND : bond 0.00457 ( 2) SS BOND : angle 1.00794 ( 4) covalent geometry : bond 0.00240 ( 9241) covalent geometry : angle 0.48164 (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 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.4574 (tpm170) cc_final: 0.3996 (ttm170) REVERT: A 279 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.4553 (t80) REVERT: D 248 LYS cc_start: 0.8826 (tttt) cc_final: 0.8320 (mmtt) REVERT: D 318 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: D 347 ASN cc_start: 0.8358 (t0) cc_final: 0.7774 (t0) REVERT: S 154 SER cc_start: 0.7505 (m) cc_final: 0.7057 (t) outliers start: 25 outliers final: 22 residues processed: 141 average time/residue: 0.2799 time to fit residues: 54.3128 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 112 MET 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 279 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 262 THR 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 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: 0.0970 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 12 optimal weight: 0.0270 chunk 94 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.1072 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.121745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096356 restraints weight = 16697.925| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.21 r_work: 0.3186 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9243 Z= 0.088 Angle : 0.450 7.404 12486 Z= 0.242 Chirality : 0.040 0.228 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.723 59.744 1261 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.01 (0.25), residues: 1133 helix: 2.67 (0.26), residues: 392 sheet: 1.09 (0.32), residues: 274 loop : -1.46 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.002 0.000 HIS S 35 PHE 0.025 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 417) hydrogen bonds : angle 3.44177 ( 1179) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.94347 ( 4) covalent geometry : bond 0.00180 ( 9241) covalent geometry : angle 0.45006 (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 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.4331 (tpm170) cc_final: 0.3730 (ttm170) REVERT: A 251 ARG cc_start: 0.8839 (tmm-80) cc_final: 0.8633 (tmm-80) REVERT: D 248 LYS cc_start: 0.8728 (tttt) cc_final: 0.8173 (mmtt) REVERT: D 347 ASN cc_start: 0.8287 (t0) cc_final: 0.7749 (t0) REVERT: S 154 SER cc_start: 0.7477 (m) cc_final: 0.7151 (p) outliers start: 15 outliers final: 13 residues processed: 136 average time/residue: 0.2402 time to fit residues: 44.4466 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 112 MET 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 C residue 58 GLU 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 234 PHE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU 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: 1.9990 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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** E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092777 restraints weight = 16477.527| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.18 r_work: 0.3127 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9243 Z= 0.108 Angle : 0.493 8.558 12486 Z= 0.262 Chirality : 0.041 0.207 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.826 58.104 1261 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.61 % Allowed : 14.99 % 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: 0.94 (0.25), residues: 1133 helix: 2.67 (0.26), residues: 392 sheet: 1.02 (0.31), residues: 276 loop : -1.54 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 82 HIS 0.005 0.001 HIS A 206 PHE 0.028 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 417) hydrogen bonds : angle 3.54079 ( 1179) SS BOND : bond 0.00465 ( 2) SS BOND : angle 0.96468 ( 4) covalent geometry : bond 0.00242 ( 9241) covalent geometry : angle 0.49251 (12482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5625.92 seconds wall clock time: 99 minutes 9.51 seconds (5949.51 seconds total)