Starting phenix.real_space_refine on Tue Feb 11 22:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.map" model { file = "/net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfz_29989/02_2025/8gfz_29989.cif" } resolution = 3.0 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= -0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4311 2.51 5 N 1154 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2433 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2147 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 4.83, per 1000 atoms: 0.72 Number of scatterers: 6744 At special positions: 0 Unit cell: (85.0346, 132.758, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1231 8.00 N 1154 7.00 C 4311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.570A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.527A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.696A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.604A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.649A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.605A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.528A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 37 through 61 Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.083A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.598A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.606A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 3.785A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.560A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.705A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.082A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.813A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.519A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.646A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.095A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.887A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.976A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1008 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: 1.87 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1737 1.33 - 1.45: 1331 1.45 - 1.57: 3747 1.57 - 1.69: 5 1.69 - 1.81: 62 Bond restraints: 6882 Sorted by residual: bond pdb=" CA GLU R 237 " pdb=" C GLU R 237 " ideal model delta sigma weight residual 1.524 1.486 0.039 1.43e-02 4.89e+03 7.26e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA GLU R 237 " pdb=" CB GLU R 237 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.34e-02 5.57e+03 6.71e+00 bond pdb=" N LYS R 235 " pdb=" CA LYS R 235 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.21e-02 6.83e+03 6.27e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 6877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 9274 1.84 - 3.68: 88 3.68 - 5.51: 23 5.51 - 7.35: 2 7.35 - 9.19: 1 Bond angle restraints: 9388 Sorted by residual: angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N ASP R 234 " pdb=" CA ASP R 234 " pdb=" C ASP R 234 " ideal model delta sigma weight residual 111.82 117.66 -5.84 1.16e+00 7.43e-01 2.53e+01 angle pdb=" O ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 121.87 117.29 4.58 9.70e-01 1.06e+00 2.23e+01 angle pdb=" CA ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 117.15 121.88 -4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" CB SER R 236 " ideal model delta sigma weight residual 110.12 105.99 4.13 1.47e+00 4.63e-01 7.89e+00 ... (remaining 9383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 3895 28.07 - 56.14: 108 56.14 - 84.22: 9 84.22 - 112.29: 0 112.29 - 140.36: 3 Dihedral angle restraints: 4015 sinusoidal: 1417 harmonic: 2598 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -35.77 140.36 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 175.06 128.74 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -57.70 126.97 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 797 0.041 - 0.082: 244 0.082 - 0.123: 61 0.123 - 0.164: 3 0.164 - 0.205: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA SER R 236 " pdb=" N SER R 236 " pdb=" C SER R 236 " pdb=" CB SER R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1103 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE R 205 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 332 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C THR R 281 " 0.023 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.008 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 510 2.74 - 3.28: 6307 3.28 - 3.82: 10683 3.82 - 4.36: 12368 4.36 - 4.90: 22591 Nonbonded interactions: 52459 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.309 3.040 ... (remaining 52454 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: 1.710 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6882 Z= 0.189 Angle : 0.500 9.190 9388 Z= 0.287 Chirality : 0.041 0.205 1106 Planarity : 0.003 0.034 1177 Dihedral : 13.528 140.362 2324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 873 helix: 1.44 (0.27), residues: 381 sheet: 0.47 (0.41), residues: 165 loop : -0.60 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 234 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.700 Fit side-chains REVERT: A 386 MET cc_start: 0.8572 (ttm) cc_final: 0.8269 (ttp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.3163 time to fit residues: 135.5841 Evaluate side-chains 81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.094718 restraints weight = 8582.752| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.82 r_work: 0.2882 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6882 Z= 0.160 Angle : 0.487 5.552 9388 Z= 0.262 Chirality : 0.041 0.131 1106 Planarity : 0.003 0.027 1177 Dihedral : 8.624 140.355 979 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.20 % Allowed : 7.51 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 873 helix: 1.78 (0.27), residues: 391 sheet: 0.56 (0.39), residues: 171 loop : -0.57 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.739 Fit side-chains REVERT: R 188 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7349 (mm-30) REVERT: R 231 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7767 (tt0) REVERT: R 239 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8078 (ptt180) outliers start: 8 outliers final: 2 residues processed: 94 average time/residue: 1.3553 time to fit residues: 133.8523 Evaluate side-chains 88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091809 restraints weight = 8723.255| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.84 r_work: 0.2838 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6882 Z= 0.218 Angle : 0.508 5.516 9388 Z= 0.271 Chirality : 0.042 0.134 1106 Planarity : 0.003 0.034 1177 Dihedral : 8.447 140.622 979 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.05 % Allowed : 10.66 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 873 helix: 1.85 (0.27), residues: 390 sheet: 0.75 (0.40), residues: 164 loop : -0.61 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.761 Fit side-chains REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.9042 (m-80) REVERT: B 303 ASP cc_start: 0.8594 (p0) cc_final: 0.8277 (p0) REVERT: R 79 ASP cc_start: 0.8492 (m-30) cc_final: 0.8155 (m-30) REVERT: R 188 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7420 (mm-30) REVERT: R 231 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8038 (tm-30) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 1.3280 time to fit residues: 128.4979 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 65 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096094 restraints weight = 8826.032| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.85 r_work: 0.2907 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6882 Z= 0.116 Angle : 0.437 5.498 9388 Z= 0.235 Chirality : 0.040 0.130 1106 Planarity : 0.003 0.028 1177 Dihedral : 8.141 138.783 979 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.20 % Allowed : 12.76 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 873 helix: 2.10 (0.27), residues: 390 sheet: 0.80 (0.39), residues: 174 loop : -0.50 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.726 Fit side-chains REVERT: A 25 LYS cc_start: 0.8005 (tttt) cc_final: 0.7730 (ttmm) REVERT: B 303 ASP cc_start: 0.8450 (p0) cc_final: 0.8121 (p0) REVERT: R 79 ASP cc_start: 0.8359 (m-30) cc_final: 0.8022 (m-30) REVERT: R 231 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.2782 time to fit residues: 119.8795 Evaluate side-chains 80 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.094652 restraints weight = 8696.823| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.83 r_work: 0.2878 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6882 Z= 0.153 Angle : 0.460 5.506 9388 Z= 0.246 Chirality : 0.041 0.129 1106 Planarity : 0.003 0.032 1177 Dihedral : 7.944 133.640 979 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.50 % Allowed : 12.76 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 873 helix: 2.15 (0.27), residues: 390 sheet: 0.87 (0.40), residues: 169 loop : -0.58 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.854 Fit side-chains REVERT: A 25 LYS cc_start: 0.7993 (tttt) cc_final: 0.7731 (ttmm) REVERT: B 303 ASP cc_start: 0.8472 (p0) cc_final: 0.8134 (p0) REVERT: R 79 ASP cc_start: 0.8404 (m-30) cc_final: 0.8039 (m-30) REVERT: R 228 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7510 (ttm110) REVERT: R 231 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7843 (tm-30) outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 1.3381 time to fit residues: 122.4968 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.096326 restraints weight = 8751.964| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.83 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6882 Z= 0.130 Angle : 0.443 5.547 9388 Z= 0.237 Chirality : 0.040 0.129 1106 Planarity : 0.003 0.029 1177 Dihedral : 7.731 130.158 979 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.50 % Allowed : 13.51 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 873 helix: 2.24 (0.27), residues: 390 sheet: 0.89 (0.40), residues: 168 loop : -0.55 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.728 Fit side-chains REVERT: A 25 LYS cc_start: 0.7827 (tttt) cc_final: 0.7588 (ttmm) REVERT: A 386 MET cc_start: 0.8814 (ttm) cc_final: 0.8401 (ttp) REVERT: R 79 ASP cc_start: 0.8338 (m-30) cc_final: 0.7982 (m-30) REVERT: R 156 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (ttp) REVERT: R 231 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7752 (tm-30) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 1.2542 time to fit residues: 113.5839 Evaluate side-chains 84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.095933 restraints weight = 8721.663| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.82 r_work: 0.2886 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6882 Z= 0.141 Angle : 0.456 5.552 9388 Z= 0.244 Chirality : 0.041 0.264 1106 Planarity : 0.003 0.030 1177 Dihedral : 7.622 127.397 979 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 13.81 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 873 helix: 2.27 (0.27), residues: 390 sheet: 0.88 (0.40), residues: 168 loop : -0.56 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.009 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.693 Fit side-chains REVERT: A 25 LYS cc_start: 0.7772 (tttt) cc_final: 0.7539 (ttmm) REVERT: A 386 MET cc_start: 0.8811 (ttm) cc_final: 0.8400 (ttp) REVERT: R 79 ASP cc_start: 0.8335 (m-30) cc_final: 0.7957 (m-30) REVERT: R 156 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: R 228 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7387 (ttm110) REVERT: R 231 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.3048 time to fit residues: 113.9042 Evaluate side-chains 84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092984 restraints weight = 8798.152| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.84 r_work: 0.2851 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6882 Z= 0.188 Angle : 0.486 5.590 9388 Z= 0.259 Chirality : 0.041 0.139 1106 Planarity : 0.003 0.033 1177 Dihedral : 7.613 125.042 979 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.95 % Allowed : 13.66 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 873 helix: 2.21 (0.27), residues: 390 sheet: 0.89 (0.40), residues: 164 loop : -0.62 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.742 Fit side-chains REVERT: A 25 LYS cc_start: 0.7842 (tttt) cc_final: 0.7592 (ttmm) REVERT: A 34 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7969 (tttp) REVERT: R 79 ASP cc_start: 0.8479 (m-30) cc_final: 0.8095 (m-30) REVERT: R 228 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7443 (ttm110) REVERT: R 231 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7806 (tm-30) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 1.4211 time to fit residues: 123.7934 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097009 restraints weight = 8776.160| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.82 r_work: 0.2898 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6882 Z= 0.123 Angle : 0.446 5.477 9388 Z= 0.239 Chirality : 0.041 0.276 1106 Planarity : 0.003 0.028 1177 Dihedral : 7.278 118.770 979 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.65 % Allowed : 14.11 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.29), residues: 873 helix: 2.37 (0.27), residues: 391 sheet: 0.83 (0.40), residues: 168 loop : -0.55 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.010 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.006 0.001 TYR A 339 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.717 Fit side-chains REVERT: A 25 LYS cc_start: 0.7683 (tttt) cc_final: 0.7472 (ttmm) REVERT: A 268 GLU cc_start: 0.7633 (tp30) cc_final: 0.6897 (tt0) REVERT: A 386 MET cc_start: 0.8735 (ttm) cc_final: 0.8322 (ttp) REVERT: R 79 ASP cc_start: 0.8472 (m-30) cc_final: 0.8110 (m-30) REVERT: R 228 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7306 (ttm110) REVERT: R 231 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 1.3360 time to fit residues: 115.5532 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.093725 restraints weight = 8913.905| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.85 r_work: 0.2874 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6882 Z= 0.176 Angle : 0.482 5.494 9388 Z= 0.257 Chirality : 0.041 0.146 1106 Planarity : 0.003 0.033 1177 Dihedral : 7.252 115.411 979 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.10 % Allowed : 14.11 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 873 helix: 2.29 (0.27), residues: 390 sheet: 0.78 (0.40), residues: 169 loop : -0.57 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.011 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.731 Fit side-chains REVERT: A 25 LYS cc_start: 0.7895 (tttt) cc_final: 0.7662 (ttmm) REVERT: A 34 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8033 (tttp) REVERT: R 228 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7528 (ttm110) REVERT: R 231 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7870 (tm-30) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 1.2326 time to fit residues: 114.2440 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092571 restraints weight = 8836.492| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.84 r_work: 0.2846 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6882 Z= 0.198 Angle : 0.495 5.495 9388 Z= 0.264 Chirality : 0.042 0.246 1106 Planarity : 0.003 0.033 1177 Dihedral : 7.199 111.725 979 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.95 % Allowed : 13.96 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 873 helix: 2.22 (0.27), residues: 390 sheet: 0.82 (0.40), residues: 164 loop : -0.62 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.011 0.001 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4992.52 seconds wall clock time: 88 minutes 51.93 seconds (5331.93 seconds total)