Starting phenix.real_space_refine on Tue Feb 11 23:27:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg5_29995/02_2025/8gg5_29995.cif" } resolution = 3.2 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= 0.027 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 47 5.16 5 C 4351 2.51 5 N 1167 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 3 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: 6799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1799 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2456 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 335 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} 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: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2157 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 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: 4.70, per 1000 atoms: 0.69 Number of scatterers: 6799 At special positions: 0 Unit cell: (85.0346, 133.626, 100.653, 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 47 16.00 P 3 15.00 O 1231 8.00 N 1167 7.00 C 4351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 1.71 Conformation dependent library (CDL) restraints added in 953.1 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.820A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.532A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.007A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.615A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.699A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.258A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.556A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.753A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.596A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.978A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.750A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 61 removed outlier: 3.702A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 67 through 86 removed outlier: 4.319A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 103 through 137 removed outlier: 4.193A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.016A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.549A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.676A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 299 removed outlier: 3.677A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.441A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.622A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.967A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.713A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.646A 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: 3.892A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A 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: 7.111A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.055A 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 153 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.335A 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: 6.838A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.778A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 993 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: 1.97 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2185 1.34 - 1.46: 1621 1.46 - 1.58: 3065 1.58 - 1.70: 5 1.70 - 1.81: 66 Bond restraints: 6942 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.435 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.563 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.318 0.035 2.00e-02 2.50e+03 3.14e+00 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 9312 1.51 - 3.02: 129 3.02 - 4.53: 25 4.53 - 6.04: 7 6.04 - 7.55: 2 Bond angle restraints: 9475 Sorted by residual: angle pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C4' GTP A 401 " ideal model delta sigma weight residual 111.00 103.45 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" C PHE B 234 " ideal model delta sigma weight residual 110.50 113.78 -3.28 1.41e+00 5.03e-01 5.42e+00 angle pdb=" N LEU R 287 " pdb=" CA LEU R 287 " pdb=" C LEU R 287 " ideal model delta sigma weight residual 109.81 114.33 -4.52 2.21e+00 2.05e-01 4.19e+00 angle pdb=" C GLU A 330 " pdb=" CA GLU A 330 " pdb=" CB GLU A 330 " ideal model delta sigma weight residual 110.36 113.80 -3.44 1.78e+00 3.16e-01 3.74e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 122.96 -6.66 3.50e+00 8.16e-02 3.62e+00 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 3976 34.79 - 69.58: 62 69.58 - 104.37: 5 104.37 - 139.16: 0 139.16 - 173.95: 1 Dihedral angle restraints: 4044 sinusoidal: 1409 harmonic: 2635 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 86.93 173.95 1 2.00e+01 2.50e-03 4.79e+01 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 11.47 93.12 1 2.00e+01 2.50e-03 2.53e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 601 0.026 - 0.052: 290 0.052 - 0.078: 145 0.078 - 0.104: 51 0.104 - 0.130: 32 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 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 2.53 -0.13 2.00e-01 2.50e+01 4.20e-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 4.01e-01 ... (remaining 1116 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO B 39 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 332 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 236 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1966 2.81 - 3.34: 5969 3.34 - 3.86: 10378 3.86 - 4.38: 11880 4.38 - 4.90: 21982 Nonbonded interactions: 52175 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.292 3.040 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.294 3.120 nonbonded pdb=" O TYR A 253 " pdb=" ND2 ASN A 264 " model vdw 2.314 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.323 3.120 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.336 3.040 ... (remaining 52170 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: 1.650 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.880 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.004 0.051 6942 Z= 0.263 Angle : 0.516 7.549 9475 Z= 0.272 Chirality : 0.042 0.130 1119 Planarity : 0.004 0.041 1186 Dihedral : 14.022 173.947 2328 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 0.36 (0.28), residues: 890 helix: 1.46 (0.27), residues: 385 sheet: -0.52 (0.39), residues: 166 loop : -0.71 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.006 0.001 HIS B 62 PHE 0.014 0.002 PHE R 49 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.709 Fit side-chains REVERT: A 27 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8339 (mt-10) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1985 time to fit residues: 22.6455 Evaluate side-chains 73 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 23 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113430 restraints weight = 8656.525| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.13 r_work: 0.2991 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6942 Z= 0.152 Angle : 0.482 7.374 9475 Z= 0.261 Chirality : 0.041 0.131 1119 Planarity : 0.003 0.035 1186 Dihedral : 7.417 173.463 993 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % 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: 890 helix: 1.69 (0.27), residues: 397 sheet: 0.03 (0.42), residues: 159 loop : -0.73 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.006 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.006 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.778 Fit side-chains REVERT: R 156 MET cc_start: 0.8322 (mtp) cc_final: 0.8097 (mtp) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.1812 time to fit residues: 21.1765 Evaluate side-chains 78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113980 restraints weight = 8672.912| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.09 r_work: 0.2968 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6942 Z= 0.184 Angle : 0.478 7.518 9475 Z= 0.255 Chirality : 0.041 0.138 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.428 175.028 993 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.90 % Allowed : 9.76 % Favored : 89.34 % 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: 0.83 (0.28), residues: 890 helix: 1.81 (0.26), residues: 397 sheet: 0.17 (0.42), residues: 159 loop : -0.77 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE R 49 TYR 0.008 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.777 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.1889 time to fit residues: 20.8524 Evaluate side-chains 77 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.0370 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113310 restraints weight = 8778.271| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.12 r_work: 0.2974 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6942 Z= 0.193 Angle : 0.484 7.514 9475 Z= 0.258 Chirality : 0.041 0.137 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.421 174.887 993 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.90 % Allowed : 12.91 % Favored : 86.19 % 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: 0.87 (0.28), residues: 890 helix: 1.86 (0.26), residues: 398 sheet: 0.18 (0.43), residues: 159 loop : -0.77 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE R 282 TYR 0.008 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.790 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 77 average time/residue: 0.1937 time to fit residues: 20.4177 Evaluate side-chains 78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 16 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115455 restraints weight = 8645.823| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.10 r_work: 0.3003 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6942 Z= 0.144 Angle : 0.447 7.348 9475 Z= 0.239 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.318 173.691 993 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.75 % Allowed : 14.11 % Favored : 85.14 % 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: 1.08 (0.28), residues: 890 helix: 2.01 (0.26), residues: 400 sheet: 0.31 (0.43), residues: 160 loop : -0.67 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.006 0.001 TYR B 105 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.776 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.1960 time to fit residues: 21.7274 Evaluate side-chains 78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112435 restraints weight = 8696.935| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.11 r_work: 0.2942 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6942 Z= 0.234 Angle : 0.495 7.560 9475 Z= 0.264 Chirality : 0.042 0.138 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.441 174.982 993 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.05 % Allowed : 15.32 % Favored : 83.63 % 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: 0.99 (0.28), residues: 890 helix: 1.96 (0.26), residues: 399 sheet: 0.16 (0.41), residues: 165 loop : -0.69 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE R 282 TYR 0.008 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.722 Fit side-chains REVERT: R 328 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7624 (mtm110) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.2010 time to fit residues: 21.6967 Evaluate side-chains 80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.0470 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115605 restraints weight = 8643.528| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.13 r_work: 0.3053 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6942 Z= 0.107 Angle : 0.425 7.181 9475 Z= 0.228 Chirality : 0.040 0.130 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.232 172.510 993 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.90 % Allowed : 15.47 % Favored : 83.63 % 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: 1.23 (0.28), residues: 890 helix: 2.22 (0.26), residues: 397 sheet: 0.38 (0.43), residues: 160 loop : -0.69 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS A 220 PHE 0.008 0.001 PHE R 217 TYR 0.005 0.001 TYR R 308 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.782 Fit side-chains REVERT: A 343 ASP cc_start: 0.8348 (m-30) cc_final: 0.7912 (m-30) REVERT: A 368 ASP cc_start: 0.6836 (p0) cc_final: 0.6595 (p0) REVERT: R 51 ASN cc_start: 0.7884 (m-40) cc_final: 0.7603 (m110) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.1992 time to fit residues: 23.0608 Evaluate side-chains 80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 137 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 6 optimal weight: 0.0060 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115777 restraints weight = 8701.603| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.10 r_work: 0.3008 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6942 Z= 0.146 Angle : 0.444 7.294 9475 Z= 0.237 Chirality : 0.040 0.133 1119 Planarity : 0.003 0.032 1186 Dihedral : 7.241 172.780 993 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.75 % Allowed : 15.77 % Favored : 83.48 % 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: 1.30 (0.28), residues: 890 helix: 2.27 (0.26), residues: 400 sheet: 0.31 (0.42), residues: 165 loop : -0.63 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR B 105 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.690 Fit side-chains REVERT: A 368 ASP cc_start: 0.6903 (p0) cc_final: 0.6690 (p0) outliers start: 5 outliers final: 5 residues processed: 76 average time/residue: 0.2147 time to fit residues: 21.8118 Evaluate side-chains 75 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 137 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112476 restraints weight = 8762.224| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.14 r_work: 0.2990 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6942 Z= 0.165 Angle : 0.451 7.361 9475 Z= 0.242 Chirality : 0.041 0.134 1119 Planarity : 0.003 0.032 1186 Dihedral : 7.279 173.366 993 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.75 % Allowed : 16.07 % Favored : 83.18 % 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: 1.28 (0.28), residues: 890 helix: 2.28 (0.26), residues: 400 sheet: 0.26 (0.41), residues: 165 loop : -0.65 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR B 105 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.700 Fit side-chains REVERT: A 368 ASP cc_start: 0.6968 (p0) cc_final: 0.6758 (p0) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2072 time to fit residues: 21.9646 Evaluate side-chains 75 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111727 restraints weight = 8847.650| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.16 r_work: 0.2979 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6942 Z= 0.174 Angle : 0.459 7.398 9475 Z= 0.245 Chirality : 0.041 0.135 1119 Planarity : 0.003 0.032 1186 Dihedral : 7.300 173.538 993 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.90 % Allowed : 16.07 % Favored : 83.03 % 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: 1.25 (0.28), residues: 890 helix: 2.29 (0.26), residues: 400 sheet: 0.19 (0.41), residues: 165 loop : -0.67 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 49 TYR 0.007 0.001 TYR B 105 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.708 Fit side-chains REVERT: A 368 ASP cc_start: 0.6966 (p0) cc_final: 0.6758 (p0) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.1943 time to fit residues: 19.8031 Evaluate side-chains 75 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118290 restraints weight = 8682.023| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.09 r_work: 0.3248 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6942 Z= 0.111 Angle : 0.419 7.132 9475 Z= 0.225 Chirality : 0.040 0.145 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.155 171.513 993 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.75 % Allowed : 16.37 % Favored : 82.88 % 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: 890 helix: 2.46 (0.26), residues: 397 sheet: 0.34 (0.42), residues: 165 loop : -0.66 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.008 0.001 PHE B 199 TYR 0.005 0.001 TYR R 308 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.95 seconds wall clock time: 68 minutes 9.11 seconds (4089.11 seconds total)