Starting phenix.real_space_refine on Mon May 12 21:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jii_36312/05_2025/8jii_36312_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jii_36312/05_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_36312/05_2025/8jii_36312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jii_36312/05_2025/8jii_36312.map" model { file = "/net/cci-nas-00/data/ceres_data/8jii_36312/05_2025/8jii_36312_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jii_36312/05_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-5687/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: 5.72, per 1000 atoms: 0.63 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: 2.43 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: 1.14 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: 2.49 Time building geometry restraints manager: 2.82 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: 0.830 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: 0.070 Set scattering table: 0.090 Process input model: 23.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.850 ------------------------------------------------------------------------------- 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 9287 Z= 0.291 Angle : 0.840 17.321 12572 Z= 0.454 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 Details of bonding type rmsd hydrogen bonds : bond 0.15078 ( 329) hydrogen bonds : angle 6.26763 ( 927) SS BOND : bond 0.00835 ( 4) SS BOND : angle 2.60923 ( 8) covalent geometry : bond 0.00588 ( 9283) covalent geometry : angle 0.83729 (12564) *********************** 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 : 1.026 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: 0.2524 time to fit residues: 41.9762 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 : 0.940 ------------------------------------------------------------------------------- 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 = 0.161951 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 = 12619.816| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.80 r_work: 0.3513 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- 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 9287 Z= 0.122 Angle : 0.602 7.744 12572 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 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 329) hydrogen bonds : angle 4.83648 ( 927) SS BOND : bond 0.00453 ( 4) SS BOND : angle 1.39966 ( 8) covalent geometry : bond 0.00275 ( 9283) covalent geometry : angle 0.60066 (12564) *********************** 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 : 0.897 Fit side-chains REVERT: B 155 ASN cc_start: 0.8460 (t0) cc_final: 0.8149 (t0) REVERT: B 262 MET cc_start: 0.7388 (ttp) cc_final: 0.7133 (ttm) REVERT: D 9 ASP cc_start: 0.8266 (m-30) cc_final: 0.8018 (m-30) REVERT: D 248 LYS cc_start: 0.7382 (mptt) cc_final: 0.7118 (mmtt) REVERT: D 308 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7233 (mt-10) REVERT: S 175 TYR cc_start: 0.7957 (m-10) cc_final: 0.7744 (m-10) REVERT: A 39 ILE cc_start: 0.8485 (tp) cc_final: 0.8111 (tp) REVERT: A 62 SER cc_start: 0.8315 (t) cc_final: 0.7958 (p) outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.2424 time to fit residues: 39.0448 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 : 0.892 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.160278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132285 restraints weight = 12947.682| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.91 r_work: 0.3518 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9287 Z= 0.112 Angle : 0.552 7.975 12572 Z= 0.289 Chirality : 0.042 0.135 1408 Planarity : 0.003 0.048 1581 Dihedral : 6.060 82.011 1321 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.54 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: -1.15 (0.25), residues: 1130 helix: -0.20 (0.30), residues: 343 sheet: -0.12 (0.30), residues: 305 loop : -1.54 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 329) hydrogen bonds : angle 4.51287 ( 927) SS BOND : bond 0.00445 ( 4) SS BOND : angle 1.36512 ( 8) covalent geometry : bond 0.00257 ( 9283) covalent geometry : angle 0.55095 (12564) *********************** 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 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.035 Fit side-chains REVERT: B 155 ASN cc_start: 0.8436 (t0) cc_final: 0.8147 (t0) REVERT: B 262 MET cc_start: 0.7691 (ttp) cc_final: 0.7323 (ttm) REVERT: D 9 ASP cc_start: 0.8296 (m-30) cc_final: 0.8067 (m-30) REVERT: D 248 LYS cc_start: 0.7413 (mptt) cc_final: 0.7109 (mmtt) REVERT: S 175 TYR cc_start: 0.7951 (m-10) cc_final: 0.7737 (m-10) REVERT: A 39 ILE cc_start: 0.8537 (tp) cc_final: 0.8162 (tp) REVERT: A 62 SER cc_start: 0.8354 (t) cc_final: 0.7939 (p) REVERT: A 92 ASP cc_start: 0.7693 (t0) cc_final: 0.7390 (t0) REVERT: A 166 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7627 (tttm) REVERT: A 270 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7802 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 133 average time/residue: 0.2589 time to fit residues: 45.8530 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 : 0.897 ------------------------------------------------------------------------------- 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: 3.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 0.0470 chunk 47 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.160651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132460 restraints weight = 12712.501| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.86 r_work: 0.3517 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9287 Z= 0.109 Angle : 0.540 8.065 12572 Z= 0.281 Chirality : 0.042 0.133 1408 Planarity : 0.003 0.046 1581 Dihedral : 5.926 81.567 1321 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.91 % Allowed : 12.17 % Favored : 86.92 % 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: -1.00 (0.25), residues: 1130 helix: -0.05 (0.30), residues: 343 sheet: -0.02 (0.30), residues: 304 loop : -1.49 (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 0.013 0.001 PHE A 240 TYR 0.017 0.001 TYR S 190 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 329) hydrogen bonds : angle 4.40250 ( 927) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.20522 ( 8) covalent geometry : bond 0.00252 ( 9283) covalent geometry : angle 0.53934 (12564) *********************** 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 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.035 Fit side-chains REVERT: B 155 ASN cc_start: 0.8465 (t0) cc_final: 0.8261 (t0) REVERT: B 262 MET cc_start: 0.7659 (ttp) cc_final: 0.7385 (mtt) REVERT: D 9 ASP cc_start: 0.8300 (m-30) cc_final: 0.8074 (m-30) REVERT: D 248 LYS cc_start: 0.7394 (mptt) cc_final: 0.7073 (mmtt) REVERT: S 175 TYR cc_start: 0.7951 (m-10) cc_final: 0.7728 (m-10) REVERT: A 62 SER cc_start: 0.8390 (t) cc_final: 0.7965 (p) REVERT: A 166 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7496 (tttm) REVERT: A 167 MET cc_start: 0.4916 (tpp) cc_final: 0.4486 (tpt) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 0.2724 time to fit residues: 43.8853 Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain A residue 159 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 125 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134213 restraints weight = 12735.005| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.75 r_work: 0.3527 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9287 Z= 0.104 Angle : 0.522 7.976 12572 Z= 0.273 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.046 1581 Dihedral : 5.816 80.567 1321 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.42 % Allowed : 12.88 % 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: -0.89 (0.25), residues: 1130 helix: 0.05 (0.30), residues: 344 sheet: 0.02 (0.30), residues: 304 loop : -1.41 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 240 TYR 0.016 0.001 TYR S 190 ARG 0.010 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 329) hydrogen bonds : angle 4.29145 ( 927) SS BOND : bond 0.00427 ( 4) SS BOND : angle 1.19992 ( 8) covalent geometry : bond 0.00239 ( 9283) covalent geometry : angle 0.52084 (12564) *********************** 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: 14 poor density : 116 time to evaluate : 1.047 Fit side-chains REVERT: B 155 ASN cc_start: 0.8480 (t0) cc_final: 0.8251 (t0) REVERT: B 262 MET cc_start: 0.7644 (ttp) cc_final: 0.7394 (mtt) REVERT: D 9 ASP cc_start: 0.8265 (m-30) cc_final: 0.8049 (m-30) REVERT: D 248 LYS cc_start: 0.7425 (mptt) cc_final: 0.7101 (mmtt) REVERT: S 97 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8535 (p) REVERT: S 175 TYR cc_start: 0.7949 (m-10) cc_final: 0.7741 (m-10) REVERT: A 89 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7261 (mtp85) REVERT: A 166 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7423 (tttm) REVERT: A 270 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7805 (ttt-90) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.2431 time to fit residues: 40.9964 Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 98 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 0.0000 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.160483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132819 restraints weight = 12628.899| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.69 r_work: 0.3495 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9287 Z= 0.149 Angle : 0.583 9.902 12572 Z= 0.301 Chirality : 0.043 0.134 1408 Planarity : 0.004 0.047 1581 Dihedral : 5.961 82.244 1321 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.72 % Allowed : 12.98 % Favored : 85.29 % 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: -0.99 (0.25), residues: 1130 helix: -0.03 (0.30), residues: 347 sheet: -0.00 (0.30), residues: 300 loop : -1.49 (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 S 35 PHE 0.013 0.001 PHE A 240 TYR 0.015 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 329) hydrogen bonds : angle 4.33730 ( 927) SS BOND : bond 0.00555 ( 4) SS BOND : angle 1.51883 ( 8) covalent geometry : bond 0.00362 ( 9283) covalent geometry : angle 0.58240 (12564) *********************** 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 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.899 Fit side-chains REVERT: B 262 MET cc_start: 0.7724 (ttp) cc_final: 0.7453 (mtt) REVERT: C 21 MET cc_start: 0.6153 (tmm) cc_final: 0.4809 (tmm) REVERT: D 9 ASP cc_start: 0.8279 (m-30) cc_final: 0.8001 (m-30) REVERT: D 248 LYS cc_start: 0.7385 (mptt) cc_final: 0.7053 (mmtt) REVERT: S 97 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (p) REVERT: S 177 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6657 (p90) REVERT: A 89 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.7235 (mtp85) REVERT: A 130 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7843 (t) REVERT: A 166 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7442 (tttm) REVERT: A 199 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7555 (mp) outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 0.2438 time to fit residues: 40.8449 Evaluate side-chains 122 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU 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: 0.6980 chunk 13 optimal weight: 0.0040 chunk 89 optimal weight: 0.0270 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 108 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4118 r_free = 0.4118 target = 0.162370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134204 restraints weight = 12878.117| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.84 r_work: 0.3546 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9287 Z= 0.089 Angle : 0.517 11.376 12572 Z= 0.266 Chirality : 0.041 0.133 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.707 78.950 1321 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.69 % 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: -0.76 (0.25), residues: 1130 helix: 0.21 (0.31), residues: 344 sheet: 0.02 (0.29), residues: 306 loop : -1.32 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS A 223 PHE 0.009 0.001 PHE B 241 TYR 0.017 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 329) hydrogen bonds : angle 4.20179 ( 927) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.17868 ( 8) covalent geometry : bond 0.00188 ( 9283) covalent geometry : angle 0.51615 (12564) *********************** 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 126 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.090 Fit side-chains REVERT: B 260 GLU cc_start: 0.5951 (tt0) cc_final: 0.5382 (tt0) REVERT: C 21 MET cc_start: 0.6319 (tmm) cc_final: 0.5045 (tmm) REVERT: D 9 ASP cc_start: 0.8053 (m-30) cc_final: 0.7765 (m-30) REVERT: D 243 MET cc_start: 0.6872 (mmt) cc_final: 0.6382 (mmt) REVERT: D 248 LYS cc_start: 0.7321 (mptt) cc_final: 0.6987 (mmtt) REVERT: S 55 SER cc_start: 0.8422 (t) cc_final: 0.8143 (t) REVERT: S 85 SER cc_start: 0.7600 (m) cc_final: 0.7348 (t) REVERT: S 177 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6121 (p90) REVERT: A 270 ARG cc_start: 0.7848 (ttt90) cc_final: 0.7560 (ttt-90) outliers start: 16 outliers final: 7 residues processed: 122 average time/residue: 0.2600 time to fit residues: 42.4351 Evaluate side-chains 114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU 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: 5.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 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 = 0.4063 r_free = 0.4063 target = 0.157727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129257 restraints weight = 12946.990| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.90 r_work: 0.3480 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9287 Z= 0.174 Angle : 0.612 9.943 12572 Z= 0.315 Chirality : 0.044 0.139 1408 Planarity : 0.004 0.046 1581 Dihedral : 6.003 83.214 1321 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.52 % Allowed : 13.79 % Favored : 84.69 % 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: -0.94 (0.25), residues: 1130 helix: -0.01 (0.30), residues: 347 sheet: 0.06 (0.30), residues: 301 loop : -1.48 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.008 0.001 HIS S 35 PHE 0.016 0.002 PHE B 234 TYR 0.016 0.002 TYR S 190 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 329) hydrogen bonds : angle 4.34879 ( 927) SS BOND : bond 0.00600 ( 4) SS BOND : angle 1.56667 ( 8) covalent geometry : bond 0.00430 ( 9283) covalent geometry : angle 0.61108 (12564) *********************** 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 127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.069 Fit side-chains REVERT: B 260 GLU cc_start: 0.6341 (tt0) cc_final: 0.6054 (tt0) REVERT: C 21 MET cc_start: 0.6079 (tmm) cc_final: 0.4904 (tmm) REVERT: D 9 ASP cc_start: 0.8318 (m-30) cc_final: 0.8046 (m-30) REVERT: D 248 LYS cc_start: 0.7386 (mptt) cc_final: 0.7065 (mmtt) REVERT: S 85 SER cc_start: 0.7782 (m) cc_final: 0.7491 (t) REVERT: S 177 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6723 (p90) REVERT: A 199 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7572 (mp) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.2505 time to fit residues: 41.7608 Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 D residue 329 THR Chi-restraints excluded: chain S residue 6 GLU 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 199 LEU 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: 0.9980 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.161307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133066 restraints weight = 12844.631| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.82 r_work: 0.3516 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9287 Z= 0.107 Angle : 0.550 9.707 12572 Z= 0.283 Chirality : 0.041 0.133 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.860 82.186 1321 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.22 % Allowed : 14.60 % Favored : 84.18 % 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: -0.82 (0.25), residues: 1130 helix: 0.09 (0.30), residues: 348 sheet: 0.11 (0.30), residues: 299 loop : -1.39 (0.27), residues: 483 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 0.018 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 329) hydrogen bonds : angle 4.26804 ( 927) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.22449 ( 8) covalent geometry : bond 0.00248 ( 9283) covalent geometry : angle 0.54946 (12564) *********************** 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 120 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.915 Fit side-chains REVERT: B 260 GLU cc_start: 0.6246 (tt0) cc_final: 0.5971 (tt0) REVERT: C 21 MET cc_start: 0.6188 (tmm) cc_final: 0.5025 (tmm) REVERT: D 9 ASP cc_start: 0.8315 (m-30) cc_final: 0.8051 (m-30) REVERT: D 248 LYS cc_start: 0.7420 (mptt) cc_final: 0.7093 (mmtt) REVERT: S 85 SER cc_start: 0.7754 (m) cc_final: 0.7492 (t) REVERT: S 177 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6553 (p90) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.2473 time to fit residues: 38.5798 Evaluate side-chains 119 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR 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 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 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.161477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133549 restraints weight = 12912.589| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.83 r_work: 0.3513 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9287 Z= 0.117 Angle : 0.559 9.446 12572 Z= 0.288 Chirality : 0.042 0.131 1408 Planarity : 0.004 0.045 1581 Dihedral : 5.843 81.975 1321 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.12 % Allowed : 14.81 % 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: -0.80 (0.25), residues: 1130 helix: 0.12 (0.30), residues: 348 sheet: 0.12 (0.30), residues: 297 loop : -1.39 (0.27), residues: 485 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 B 234 TYR 0.017 0.001 TYR S 190 ARG 0.009 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 329) hydrogen bonds : angle 4.23986 ( 927) SS BOND : bond 0.00472 ( 4) SS BOND : angle 1.37140 ( 8) covalent geometry : bond 0.00277 ( 9283) covalent geometry : angle 0.55842 (12564) ********************** 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 119 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.034 Fit side-chains REVERT: B 260 GLU cc_start: 0.6205 (tt0) cc_final: 0.5941 (tt0) REVERT: C 21 MET cc_start: 0.6111 (tmm) cc_final: 0.4986 (tmm) REVERT: D 9 ASP cc_start: 0.8321 (m-30) cc_final: 0.8054 (m-30) REVERT: D 248 LYS cc_start: 0.7391 (mptt) cc_final: 0.7061 (mmtt) REVERT: S 85 SER cc_start: 0.7724 (m) cc_final: 0.7450 (t) REVERT: S 177 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6542 (p90) outliers start: 11 outliers final: 10 residues processed: 116 average time/residue: 0.2440 time to fit residues: 38.3648 Evaluate side-chains 118 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR 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 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 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.158965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131185 restraints weight = 12776.142| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.77 r_work: 0.3471 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9287 Z= 0.205 Angle : 0.645 9.827 12572 Z= 0.331 Chirality : 0.045 0.137 1408 Planarity : 0.004 0.047 1581 Dihedral : 6.154 84.447 1321 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.62 % Allowed : 14.71 % Favored : 83.67 % 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: -1.00 (0.25), residues: 1130 helix: -0.04 (0.30), residues: 347 sheet: 0.00 (0.30), residues: 300 loop : -1.51 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.010 0.001 HIS A 133 PHE 0.017 0.002 PHE S 29 TYR 0.017 0.002 TYR S 190 ARG 0.010 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 329) hydrogen bonds : angle 4.41623 ( 927) SS BOND : bond 0.00650 ( 4) SS BOND : angle 1.73633 ( 8) covalent geometry : bond 0.00512 ( 9283) covalent geometry : angle 0.64367 (12564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5592.76 seconds wall clock time: 97 minutes 9.38 seconds (5829.38 seconds total)