Starting phenix.real_space_refine on Thu Mar 13 23:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312.map" model { file = "/net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jii_36312/03_2025/8jii_36312_neut.cif" } resolution = 3.17 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= 0.022 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5806 2.51 5 N 1543 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" 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: "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: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'IX8': 1, 'NIO': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 5.89, per 1000 atoms: 0.65 Number of scatterers: 9083 At special positions: 0 Unit cell: (93.5, 119.85, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1665 8.00 N 1543 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 32.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.554A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.558A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 26 removed outlier: 3.835A pdb=" N GLU D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.547A pdb=" N MET D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.538A pdb=" N TRP D 211 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.551A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.629A pdb=" N PHE D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 4.153A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 329 through 349 removed outlier: 3.624A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.650A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.561A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 52 removed outlier: 3.662A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.876A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.837A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.580A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.258A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.759A pdb=" N ILE A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.323A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.920A pdb=" N LYS A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.516A pdb=" N GLY A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.590A pdb=" N LEU A 162 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 removed outlier: 3.574A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.998A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.962A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 245 through 261 removed outlier: 3.741A pdb=" N VAL A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.685A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 280 removed outlier: 4.253A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.728A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.760A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.011A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.647A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.074A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.677A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.423A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 6.102A pdb=" N VAL D 34 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE D 199 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 36 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (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 58 through 60 removed outlier: 4.947A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.650A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.516A pdb=" N CYS A 18 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.747A pdb=" N ILE A 169 " --> pdb=" O LEU A 176 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1275 1.25 - 1.39: 2517 1.39 - 1.53: 5075 1.53 - 1.68: 316 1.68 - 1.82: 100 Bond restraints: 9283 Sorted by residual: bond pdb=" C9 IX8 A 403 " pdb=" N10 IX8 A 403 " ideal model delta sigma weight residual 1.386 1.266 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C27 IX8 A 403 " pdb=" C32 IX8 A 403 " ideal model delta sigma weight residual 1.396 1.277 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 IX8 A 403 " pdb=" O5 IX8 A 403 " ideal model delta sigma weight residual 1.221 1.104 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C2 IX8 A 403 " pdb=" C25 IX8 A 403 " ideal model delta sigma weight residual 1.522 1.428 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C27 IX8 A 403 " pdb=" C28 IX8 A 403 " ideal model delta sigma weight residual 1.393 1.302 0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 12467 3.46 - 6.93: 86 6.93 - 10.39: 6 10.39 - 13.86: 3 13.86 - 17.32: 2 Bond angle restraints: 12564 Sorted by residual: angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 111.90 106.74 5.16 8.10e-01 1.52e+00 4.06e+01 angle pdb=" N ILE A 77 " pdb=" CA ILE A 77 " pdb=" C ILE A 77 " ideal model delta sigma weight residual 111.62 106.70 4.92 7.90e-01 1.60e+00 3.88e+01 angle pdb=" C6 IX8 A 403 " pdb=" C4 IX8 A 403 " pdb=" N3 IX8 A 403 " ideal model delta sigma weight residual 114.73 132.05 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C23 IX8 A 403 " pdb=" C22 IX8 A 403 " pdb=" C24 IX8 A 403 " ideal model delta sigma weight residual 110.88 95.43 15.45 3.00e+00 1.11e-01 2.65e+01 ... (remaining 12559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4983 17.89 - 35.79: 470 35.79 - 53.68: 75 53.68 - 71.57: 14 71.57 - 89.46: 5 Dihedral angle restraints: 5547 sinusoidal: 2235 harmonic: 3312 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C SER A 179 " pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 5544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1010 0.047 - 0.093: 310 0.093 - 0.140: 80 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA GLU D 298 " pdb=" N GLU D 298 " pdb=" C GLU D 298 " pdb=" CB GLU D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA SER A 178 " pdb=" N SER A 178 " pdb=" C SER A 178 " pdb=" CB SER A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1405 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 IX8 A 403 " 0.015 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" C4 IX8 A 403 " -0.060 2.00e-02 2.50e+03 pdb=" C6 IX8 A 403 " 0.029 2.00e-02 2.50e+03 pdb=" N3 IX8 A 403 " 0.002 2.00e-02 2.50e+03 pdb=" O5 IX8 A 403 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CG ASP B 118 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO S 75 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 56 2.55 - 3.14: 6785 3.14 - 3.73: 12728 3.73 - 4.31: 18178 4.31 - 4.90: 32021 Nonbonded interactions: 69768 Sorted by model distance: nonbonded pdb=" O SER D 293 " pdb=" OD1 ASN D 294 " model vdw 1.963 3.040 nonbonded pdb=" NE2 GLN D 304 " pdb=" OE2 GLU D 308 " model vdw 2.197 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.269 3.040 nonbonded pdb=" OG SER A 62 " pdb=" OD2 ASP A 124 " model vdw 2.283 3.040 nonbonded pdb=" OE2 GLU D 8 " pdb=" OH TYR S 175 " model vdw 2.294 3.040 ... (remaining 69763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.006 0.120 9283 Z= 0.383 Angle : 0.837 17.321 12564 Z= 0.453 Chirality : 0.047 0.233 1408 Planarity : 0.004 0.058 1581 Dihedral : 14.119 89.464 3395 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.97 (0.24), residues: 1130 helix: -0.86 (0.29), residues: 325 sheet: -0.58 (0.29), residues: 301 loop : -2.01 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 47 HIS 0.011 0.001 HIS A 223 PHE 0.015 0.002 PHE B 234 TYR 0.028 0.002 TYR A 87 ARG 0.008 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6785 (ttp) cc_final: 0.6464 (ttm) REVERT: D 9 ASP cc_start: 0.7642 (m-30) cc_final: 0.7297 (m-30) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2527 time to fit residues: 42.3180 Evaluate side-chains 109 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.161950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134127 restraints weight = 12619.818| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.80 r_work: 0.3514 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9283 Z= 0.184 Angle : 0.601 7.744 12564 Z= 0.311 Chirality : 0.043 0.139 1408 Planarity : 0.004 0.049 1581 Dihedral : 6.348 82.485 1321 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.61 % Allowed : 5.98 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1130 helix: -0.43 (0.30), residues: 335 sheet: -0.26 (0.30), residues: 305 loop : -1.68 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE A 240 TYR 0.018 0.001 TYR S 190 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.896 Fit side-chains REVERT: B 155 ASN cc_start: 0.8456 (t0) cc_final: 0.8146 (t0) REVERT: B 262 MET cc_start: 0.7384 (ttp) cc_final: 0.7130 (ttm) REVERT: D 9 ASP cc_start: 0.8269 (m-30) cc_final: 0.8022 (m-30) REVERT: D 248 LYS cc_start: 0.7394 (mptt) cc_final: 0.7132 (mmtt) REVERT: D 308 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7222 (mt-10) REVERT: S 175 TYR cc_start: 0.7969 (m-10) cc_final: 0.7759 (m-10) REVERT: A 39 ILE cc_start: 0.8483 (tp) cc_final: 0.8110 (tp) REVERT: A 62 SER cc_start: 0.8314 (t) cc_final: 0.7955 (p) outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.2457 time to fit residues: 39.7348 Evaluate side-chains 115 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132517 restraints weight = 12951.215| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.91 r_work: 0.3522 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9283 Z= 0.163 Angle : 0.544 7.919 12564 Z= 0.286 Chirality : 0.042 0.134 1408 Planarity : 0.003 0.048 1581 Dihedral : 6.038 81.768 1321 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.61 % Allowed : 10.65 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.13 (0.25), residues: 1130 helix: -0.19 (0.30), residues: 343 sheet: -0.11 (0.30), residues: 305 loop : -1.53 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE A 240 TYR 0.018 0.001 TYR S 190 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.979 Fit side-chains REVERT: B 155 ASN cc_start: 0.8434 (t0) cc_final: 0.8142 (t0) REVERT: B 262 MET cc_start: 0.7685 (ttp) cc_final: 0.7318 (ttm) REVERT: D 9 ASP cc_start: 0.8288 (m-30) cc_final: 0.8057 (m-30) REVERT: D 248 LYS cc_start: 0.7383 (mptt) cc_final: 0.7080 (mmtt) REVERT: S 175 TYR cc_start: 0.7942 (m-10) cc_final: 0.7733 (m-10) REVERT: A 39 ILE cc_start: 0.8543 (tp) cc_final: 0.8168 (tp) REVERT: A 62 SER cc_start: 0.8358 (t) cc_final: 0.7941 (p) REVERT: A 92 ASP cc_start: 0.7706 (t0) cc_final: 0.7416 (t0) REVERT: A 166 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7621 (tttm) REVERT: A 270 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7786 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.2581 time to fit residues: 45.3258 Evaluate side-chains 120 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131556 restraints weight = 12590.883| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.73 r_work: 0.3485 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9283 Z= 0.285 Angle : 0.605 7.786 12564 Z= 0.313 Chirality : 0.044 0.135 1408 Planarity : 0.004 0.047 1581 Dihedral : 6.153 83.905 1321 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.22 % Allowed : 11.97 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.17 (0.25), residues: 1130 helix: -0.23 (0.30), residues: 346 sheet: -0.09 (0.30), residues: 302 loop : -1.57 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.007 0.001 HIS S 35 PHE 0.016 0.002 PHE A 240 TYR 0.016 0.002 TYR S 190 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.528 Fit side-chains REVERT: B 124 TYR cc_start: 0.8689 (m-80) cc_final: 0.8484 (m-80) REVERT: B 155 ASN cc_start: 0.8512 (t0) cc_final: 0.8293 (t0) REVERT: B 262 MET cc_start: 0.7724 (ttp) cc_final: 0.7424 (mtt) REVERT: D 9 ASP cc_start: 0.8308 (m-30) cc_final: 0.8076 (m-30) REVERT: D 248 LYS cc_start: 0.7433 (mptt) cc_final: 0.7104 (mmtt) REVERT: A 166 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7554 (tttm) REVERT: A 167 MET cc_start: 0.5028 (tpp) cc_final: 0.4525 (tpt) outliers start: 12 outliers final: 10 residues processed: 125 average time/residue: 0.3629 time to fit residues: 61.4411 Evaluate side-chains 122 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133329 restraints weight = 12711.023| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.77 r_work: 0.3518 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9283 Z= 0.162 Angle : 0.526 8.081 12564 Z= 0.275 Chirality : 0.041 0.133 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.942 81.762 1321 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.72 % Allowed : 12.58 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1130 helix: -0.02 (0.30), residues: 343 sheet: -0.05 (0.30), residues: 304 loop : -1.44 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 240 TYR 0.016 0.001 TYR S 190 ARG 0.010 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 2.782 Fit side-chains REVERT: B 155 ASN cc_start: 0.8495 (t0) cc_final: 0.8292 (t0) REVERT: B 262 MET cc_start: 0.7629 (ttp) cc_final: 0.7368 (mtt) REVERT: D 9 ASP cc_start: 0.8269 (m-30) cc_final: 0.8047 (m-30) REVERT: D 248 LYS cc_start: 0.7393 (mptt) cc_final: 0.7058 (mmtt) REVERT: S 175 TYR cc_start: 0.7936 (m-10) cc_final: 0.7704 (m-10) REVERT: A 166 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7383 (tttm) REVERT: A 167 MET cc_start: 0.5046 (tpp) cc_final: 0.4660 (tpt) REVERT: A 270 ARG cc_start: 0.8187 (ttt90) cc_final: 0.7836 (ttt-90) outliers start: 17 outliers final: 10 residues processed: 125 average time/residue: 0.4876 time to fit residues: 83.4298 Evaluate side-chains 117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131820 restraints weight = 12618.578| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.71 r_work: 0.3488 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9283 Z= 0.256 Angle : 0.590 10.401 12564 Z= 0.304 Chirality : 0.043 0.135 1408 Planarity : 0.004 0.046 1581 Dihedral : 6.056 83.083 1321 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.72 % Allowed : 13.08 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.04 (0.25), residues: 1130 helix: -0.09 (0.30), residues: 347 sheet: -0.06 (0.30), residues: 302 loop : -1.49 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.007 0.001 HIS S 35 PHE 0.014 0.002 PHE A 240 TYR 0.015 0.001 TYR S 190 ARG 0.007 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.985 Fit side-chains REVERT: B 124 TYR cc_start: 0.8702 (m-80) cc_final: 0.8476 (m-80) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 262 MET cc_start: 0.7724 (ttp) cc_final: 0.7451 (mtt) REVERT: D 9 ASP cc_start: 0.8308 (m-30) cc_final: 0.8025 (m-30) REVERT: D 248 LYS cc_start: 0.7417 (mptt) cc_final: 0.7074 (mmtt) REVERT: S 45 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6494 (pp) REVERT: S 97 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (p) REVERT: S 177 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6741 (p90) REVERT: A 166 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7381 (tttm) REVERT: A 167 MET cc_start: 0.5125 (tpp) cc_final: 0.4904 (tpp) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.2644 time to fit residues: 43.3009 Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132007 restraints weight = 12847.198| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.87 r_work: 0.3511 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9283 Z= 0.169 Angle : 0.532 9.323 12564 Z= 0.277 Chirality : 0.042 0.132 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.905 81.448 1321 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.83 % Allowed : 13.59 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1130 helix: 0.04 (0.30), residues: 347 sheet: -0.01 (0.30), residues: 304 loop : -1.36 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS A 133 PHE 0.011 0.001 PHE A 240 TYR 0.017 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.024 Fit side-chains REVERT: B 234 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 262 MET cc_start: 0.7678 (ttp) cc_final: 0.7420 (mtt) REVERT: C 21 MET cc_start: 0.6143 (tmm) cc_final: 0.4873 (tmm) REVERT: D 9 ASP cc_start: 0.8307 (m-30) cc_final: 0.8036 (m-30) REVERT: D 248 LYS cc_start: 0.7386 (mptt) cc_final: 0.7036 (mmtt) REVERT: S 97 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8545 (p) REVERT: S 175 TYR cc_start: 0.7939 (m-10) cc_final: 0.7698 (m-10) REVERT: S 177 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6567 (p90) REVERT: A 167 MET cc_start: 0.5118 (tpp) cc_final: 0.4903 (tpp) REVERT: A 270 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7809 (ttt-90) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.2444 time to fit residues: 38.2777 Evaluate side-chains 117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 chunk 50 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.159204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130790 restraints weight = 12987.242| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.88 r_work: 0.3490 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9283 Z= 0.227 Angle : 0.569 11.740 12564 Z= 0.293 Chirality : 0.043 0.137 1408 Planarity : 0.004 0.045 1581 Dihedral : 5.964 81.745 1321 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.93 % Allowed : 13.59 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.93 (0.25), residues: 1130 helix: 0.02 (0.30), residues: 348 sheet: 0.03 (0.30), residues: 299 loop : -1.46 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.007 0.001 HIS A 133 PHE 0.013 0.001 PHE A 240 TYR 0.016 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.992 Fit side-chains REVERT: B 234 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 260 GLU cc_start: 0.6460 (tt0) cc_final: 0.6240 (tt0) REVERT: B 262 MET cc_start: 0.7718 (ttp) cc_final: 0.7454 (mtt) REVERT: C 21 MET cc_start: 0.6111 (tmm) cc_final: 0.4904 (tmm) REVERT: D 9 ASP cc_start: 0.8316 (m-30) cc_final: 0.8045 (m-30) REVERT: D 248 LYS cc_start: 0.7403 (mptt) cc_final: 0.7052 (mmtt) REVERT: S 97 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8554 (p) REVERT: S 175 TYR cc_start: 0.7961 (m-10) cc_final: 0.7724 (m-10) REVERT: S 177 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.6682 (p90) REVERT: A 84 MET cc_start: 0.6694 (ttt) cc_final: 0.6370 (ttt) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.2500 time to fit residues: 39.6009 Evaluate side-chains 119 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130450 restraints weight = 12791.205| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.75 r_work: 0.3468 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9283 Z= 0.325 Angle : 0.640 10.904 12564 Z= 0.329 Chirality : 0.045 0.139 1408 Planarity : 0.004 0.046 1581 Dihedral : 6.247 84.728 1321 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.93 % Allowed : 14.10 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.07 (0.25), residues: 1130 helix: -0.09 (0.30), residues: 347 sheet: -0.08 (0.30), residues: 300 loop : -1.52 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.009 0.001 HIS A 133 PHE 0.016 0.002 PHE A 240 TYR 0.016 0.002 TYR S 190 ARG 0.009 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.009 Fit side-chains REVERT: B 124 TYR cc_start: 0.8746 (m-80) cc_final: 0.8505 (m-80) REVERT: B 234 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 260 GLU cc_start: 0.6530 (tt0) cc_final: 0.6312 (tt0) REVERT: B 262 MET cc_start: 0.7777 (ttp) cc_final: 0.7511 (mtt) REVERT: C 21 MET cc_start: 0.6175 (tmm) cc_final: 0.5014 (tmm) REVERT: D 9 ASP cc_start: 0.8337 (m-30) cc_final: 0.8070 (m-30) REVERT: S 97 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (p) REVERT: S 177 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6937 (p90) REVERT: A 89 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7206 (mtp180) REVERT: A 167 MET cc_start: 0.5401 (tpt) cc_final: 0.5115 (tpt) outliers start: 19 outliers final: 15 residues processed: 124 average time/residue: 0.2593 time to fit residues: 42.9396 Evaluate side-chains 127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131171 restraints weight = 12851.201| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.75 r_work: 0.3476 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9283 Z= 0.304 Angle : 0.623 11.019 12564 Z= 0.322 Chirality : 0.044 0.138 1408 Planarity : 0.004 0.046 1581 Dihedral : 6.249 83.856 1321 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.03 % Allowed : 13.89 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.13 (0.25), residues: 1130 helix: -0.20 (0.30), residues: 351 sheet: -0.12 (0.30), residues: 300 loop : -1.52 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.008 0.001 HIS A 133 PHE 0.015 0.002 PHE A 240 TYR 0.015 0.002 TYR S 190 ARG 0.009 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.967 Fit side-chains REVERT: B 124 TYR cc_start: 0.8715 (m-80) cc_final: 0.8463 (m-80) REVERT: B 234 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: B 260 GLU cc_start: 0.6501 (tt0) cc_final: 0.6285 (tt0) REVERT: B 262 MET cc_start: 0.7776 (ttp) cc_final: 0.7522 (mtt) REVERT: C 21 MET cc_start: 0.6171 (tmm) cc_final: 0.5046 (tmm) REVERT: D 9 ASP cc_start: 0.8272 (m-30) cc_final: 0.7979 (m-30) REVERT: D 248 LYS cc_start: 0.7420 (mptt) cc_final: 0.7039 (mmtt) REVERT: S 97 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (p) REVERT: S 177 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.6923 (p90) REVERT: A 89 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7176 (mtp85) REVERT: A 167 MET cc_start: 0.5376 (tpt) cc_final: 0.5057 (tpt) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.2574 time to fit residues: 41.2188 Evaluate side-chains 126 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127250 restraints weight = 12681.813| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.93 r_work: 0.3427 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9283 Z= 0.429 Angle : 0.706 11.254 12564 Z= 0.362 Chirality : 0.047 0.142 1408 Planarity : 0.004 0.047 1581 Dihedral : 6.530 85.823 1321 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.03 % Allowed : 14.20 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.29 (0.25), residues: 1130 helix: -0.26 (0.30), residues: 345 sheet: -0.20 (0.30), residues: 302 loop : -1.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.011 0.002 HIS A 133 PHE 0.021 0.002 PHE S 29 TYR 0.015 0.002 TYR S 190 ARG 0.009 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6155.22 seconds wall clock time: 107 minutes 38.24 seconds (6458.24 seconds total)