Starting phenix.real_space_refine on Tue Mar 11 18:59:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.map" model { file = "/net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unl_42408/03_2025/8unl_42408.cif" } resolution = 3.3 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 40 5.16 5 C 4219 2.51 5 N 1122 2.21 5 O 1166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1692 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 4 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 161 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2400 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 320 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2090 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.54, per 1000 atoms: 0.69 Number of scatterers: 6550 At special positions: 0 Unit cell: (83.2992, 134.493, 97.1824, 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 40 16.00 P 3 15.00 O 1166 8.00 N 1122 7.00 C 4219 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: 1.60 Conformation dependent library (CDL) restraints added in 845.5 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 47.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.876A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.506A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.864A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.829A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.790A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.505A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.321A 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 6 through 26 removed outlier: 3.815A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.516A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.854A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.538A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.525A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.678A 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 102 through 137 removed outlier: 3.926A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.536A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.608A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.576A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.546A pdb=" N ARG R 175 " --> pdb=" O HIS R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.872A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.821A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.489A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.538A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.113A 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 removed outlier: 3.575A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.218A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.593A 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: 6.656A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.094A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.973A 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 150 removed outlier: 6.878A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.713A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.681A 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: 3.586A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1005 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: 1.66 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1033 1.32 - 1.44: 1900 1.44 - 1.56: 3696 1.56 - 1.69: 7 1.69 - 1.81: 54 Bond restraints: 6690 Sorted by residual: bond pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.18e-02 7.18e+03 2.60e+01 bond pdb=" CA ASN R 148 " pdb=" C ASN R 148 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.23e-02 6.61e+03 2.34e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 ... (remaining 6685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 9019 2.36 - 4.71: 95 4.71 - 7.07: 31 7.07 - 9.42: 6 9.42 - 11.78: 3 Bond angle restraints: 9154 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.28 123.06 -11.78 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.28 118.61 -7.33 1.09e+00 8.42e-01 4.53e+01 angle pdb=" N THR A 320 " pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 110.08 101.63 8.45 1.38e+00 5.25e-01 3.75e+01 angle pdb=" N SER R 143 " pdb=" CA SER R 143 " pdb=" C SER R 143 " ideal model delta sigma weight residual 111.28 117.78 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N THR R 146 " pdb=" CA THR R 146 " pdb=" C THR R 146 " ideal model delta sigma weight residual 109.50 100.99 8.51 1.58e+00 4.01e-01 2.90e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 3780 31.00 - 62.01: 71 62.01 - 93.01: 2 93.01 - 124.02: 0 124.02 - 155.02: 5 Dihedral angle restraints: 3858 sinusoidal: 1250 harmonic: 2608 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 -50.43 155.02 1 2.00e+01 2.50e-03 4.58e+01 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 260.87 124.05 136.82 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual -85.88 44.74 -130.62 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 838 0.046 - 0.091: 205 0.091 - 0.137: 57 0.137 - 0.182: 4 0.182 - 0.228: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA HIS A 357 " pdb=" N HIS A 357 " pdb=" C HIS A 357 " pdb=" CB HIS A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 1102 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.070 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 361 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 360 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C TYR A 360 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR A 360 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 361 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO A 321 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.030 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1070 2.76 - 3.30: 6023 3.30 - 3.83: 10314 3.83 - 4.37: 11100 4.37 - 4.90: 21096 Nonbonded interactions: 49603 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.344 3.040 ... (remaining 49598 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: 1.430 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.490 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.005 0.086 6690 Z= 0.307 Angle : 0.679 11.780 9154 Z= 0.419 Chirality : 0.043 0.228 1105 Planarity : 0.005 0.110 1138 Dihedral : 14.030 155.022 2159 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.49 (0.29), residues: 874 helix: 2.56 (0.27), residues: 380 sheet: 0.66 (0.43), residues: 160 loop : -0.74 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.011 0.001 HIS R 296 PHE 0.010 0.001 PHE R 49 TYR 0.011 0.001 TYR R 141 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.767 Fit side-chains REVERT: A 350 THR cc_start: 0.8696 (m) cc_final: 0.8468 (p) REVERT: A 369 THR cc_start: 0.8647 (p) cc_final: 0.8419 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1548 time to fit residues: 18.3860 Evaluate side-chains 74 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN R 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104344 restraints weight = 9500.954| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.66 r_work: 0.3085 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6690 Z= 0.163 Angle : 0.468 5.524 9154 Z= 0.251 Chirality : 0.040 0.138 1105 Planarity : 0.003 0.037 1138 Dihedral : 9.406 144.281 975 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 7.12 % Favored : 91.56 % 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: 1.60 (0.29), residues: 874 helix: 2.58 (0.27), residues: 394 sheet: 0.93 (0.45), residues: 146 loop : -0.77 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR A 358 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.744 Fit side-chains REVERT: B 258 ASP cc_start: 0.8680 (t0) cc_final: 0.8385 (t0) REVERT: R 82 MET cc_start: 0.8438 (ttm) cc_final: 0.8138 (ttp) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1431 time to fit residues: 16.7109 Evaluate side-chains 77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102574 restraints weight = 9748.721| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.64 r_work: 0.3051 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6690 Z= 0.221 Angle : 0.476 5.531 9154 Z= 0.256 Chirality : 0.041 0.141 1105 Planarity : 0.003 0.038 1138 Dihedral : 8.152 141.652 975 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.49 % Allowed : 8.94 % Favored : 89.57 % 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: 1.53 (0.29), residues: 874 helix: 2.57 (0.27), residues: 394 sheet: 0.50 (0.42), residues: 165 loop : -0.74 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.019 0.001 TYR B 59 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.715 Fit side-chains REVERT: B 258 ASP cc_start: 0.8760 (t0) cc_final: 0.8466 (t0) REVERT: R 82 MET cc_start: 0.8493 (ttm) cc_final: 0.8206 (ttp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.1275 time to fit residues: 14.9602 Evaluate side-chains 74 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102989 restraints weight = 9793.117| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.62 r_work: 0.3050 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6690 Z= 0.207 Angle : 0.457 5.535 9154 Z= 0.247 Chirality : 0.041 0.139 1105 Planarity : 0.003 0.039 1138 Dihedral : 7.556 136.652 975 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.49 % Allowed : 10.93 % Favored : 87.58 % 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: 1.47 (0.29), residues: 874 helix: 2.54 (0.27), residues: 394 sheet: 0.49 (0.41), residues: 163 loop : -0.80 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR A 358 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.685 Fit side-chains REVERT: B 258 ASP cc_start: 0.8746 (t0) cc_final: 0.8454 (t0) REVERT: R 82 MET cc_start: 0.8459 (ttm) cc_final: 0.8144 (ttp) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.1310 time to fit residues: 14.9350 Evaluate side-chains 76 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.0270 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104309 restraints weight = 9721.313| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.84 r_work: 0.3062 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6690 Z= 0.116 Angle : 0.416 5.538 9154 Z= 0.225 Chirality : 0.039 0.131 1105 Planarity : 0.003 0.038 1138 Dihedral : 7.199 132.457 975 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.32 % Allowed : 11.09 % Favored : 87.58 % 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: 1.62 (0.30), residues: 874 helix: 2.67 (0.27), residues: 395 sheet: 0.59 (0.43), residues: 158 loop : -0.75 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS R 178 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR B 59 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.741 Fit side-chains REVERT: B 258 ASP cc_start: 0.8701 (t0) cc_final: 0.8394 (t0) REVERT: R 82 MET cc_start: 0.8384 (ttm) cc_final: 0.7989 (ttp) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.1475 time to fit residues: 17.3998 Evaluate side-chains 76 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105009 restraints weight = 9629.917| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.62 r_work: 0.3080 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.138 Angle : 0.426 5.473 9154 Z= 0.231 Chirality : 0.040 0.132 1105 Planarity : 0.003 0.037 1138 Dihedral : 6.916 130.052 975 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.49 % Allowed : 11.75 % Favored : 86.75 % 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: 1.61 (0.29), residues: 874 helix: 2.67 (0.27), residues: 395 sheet: 0.66 (0.43), residues: 156 loop : -0.80 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR B 59 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.658 Fit side-chains REVERT: B 258 ASP cc_start: 0.8673 (t0) cc_final: 0.8381 (t0) REVERT: R 82 MET cc_start: 0.8512 (ttm) cc_final: 0.8097 (ttp) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1357 time to fit residues: 15.7227 Evaluate side-chains 75 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 87 optimal weight: 0.0570 chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 60 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.126073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106175 restraints weight = 9720.543| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.82 r_work: 0.3092 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.115 Angle : 0.420 7.907 9154 Z= 0.222 Chirality : 0.039 0.131 1105 Planarity : 0.002 0.036 1138 Dihedral : 6.461 123.804 975 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 12.09 % Favored : 86.59 % 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: 1.72 (0.30), residues: 874 helix: 2.76 (0.27), residues: 395 sheet: 0.67 (0.43), residues: 157 loop : -0.74 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.000 HIS R 178 PHE 0.010 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.711 Fit side-chains REVERT: B 258 ASP cc_start: 0.8684 (t0) cc_final: 0.8353 (t0) outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 0.1372 time to fit residues: 17.8197 Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101455 restraints weight = 9812.296| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.81 r_work: 0.3020 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6690 Z= 0.254 Angle : 0.481 6.944 9154 Z= 0.256 Chirality : 0.041 0.138 1105 Planarity : 0.003 0.036 1138 Dihedral : 6.574 124.785 975 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 12.58 % Favored : 85.10 % 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 (0.30), residues: 874 helix: 2.63 (0.27), residues: 394 sheet: 0.40 (0.42), residues: 169 loop : -0.72 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.011 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.777 Fit side-chains REVERT: B 258 ASP cc_start: 0.8784 (t0) cc_final: 0.8408 (t0) outliers start: 14 outliers final: 13 residues processed: 79 average time/residue: 0.1325 time to fit residues: 15.7452 Evaluate side-chains 85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101477 restraints weight = 9859.117| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.83 r_work: 0.3037 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6690 Z= 0.225 Angle : 0.472 7.150 9154 Z= 0.252 Chirality : 0.041 0.139 1105 Planarity : 0.003 0.038 1138 Dihedral : 6.527 123.602 975 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.99 % Allowed : 12.75 % Favored : 85.26 % 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: 874 helix: 2.55 (0.27), residues: 394 sheet: 0.38 (0.42), residues: 168 loop : -0.74 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 222 TYR 0.011 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.673 Fit side-chains REVERT: B 258 ASP cc_start: 0.8779 (t0) cc_final: 0.8403 (t0) outliers start: 12 outliers final: 12 residues processed: 79 average time/residue: 0.1345 time to fit residues: 15.9356 Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 75 GLN ** 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 = 0.3413 r_free = 0.3413 target = 0.121685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101939 restraints weight = 9917.302| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6690 Z= 0.198 Angle : 0.461 6.991 9154 Z= 0.246 Chirality : 0.040 0.136 1105 Planarity : 0.003 0.037 1138 Dihedral : 6.433 121.940 975 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.66 % Allowed : 13.91 % Favored : 84.44 % 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: 874 helix: 2.58 (0.27), residues: 394 sheet: 0.55 (0.43), residues: 156 loop : -0.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.711 Fit side-chains REVERT: B 258 ASP cc_start: 0.8760 (t0) cc_final: 0.8401 (t0) outliers start: 10 outliers final: 10 residues processed: 79 average time/residue: 0.1300 time to fit residues: 15.4048 Evaluate side-chains 82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 75 GLN ** 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 = 0.3438 r_free = 0.3438 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103852 restraints weight = 10010.170| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.86 r_work: 0.3071 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6690 Z= 0.137 Angle : 0.433 6.735 9154 Z= 0.230 Chirality : 0.040 0.131 1105 Planarity : 0.003 0.037 1138 Dihedral : 6.102 116.322 975 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.49 % Allowed : 14.07 % Favored : 84.44 % 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: 1.62 (0.30), residues: 874 helix: 2.67 (0.27), residues: 395 sheet: 0.43 (0.42), residues: 168 loop : -0.68 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.000 HIS R 178 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3645.76 seconds wall clock time: 63 minutes 20.47 seconds (3800.47 seconds total)