Starting phenix.real_space_refine on Tue Feb 11 21:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.map" model { file = "/net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unr_42414/02_2025/8unr_42414.cif" } resolution = 3.4 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= 0.023 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 38 5.16 5 C 4286 2.51 5 N 1157 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6670 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1740 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1728 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 183 Conformer: "B" Number of residues, atoms: 240, 1728 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 183 bond proxies already assigned to first conformer: 1747 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2418 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 351 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2112 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.46, per 1000 atoms: 0.82 Number of scatterers: 6670 At special positions: 0 Unit cell: (85.9023, 135.361, 99.7855, 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 38 16.00 P 3 15.00 O 1186 8.00 N 1157 7.00 C 4286 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: 2.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.967A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.540A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.757A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.591A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.753A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.366A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.906A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.502A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.521A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.624A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.626A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.801A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.558A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.523A 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: 4.020A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.592A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.548A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.509A 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 removed outlier: 3.721A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.774A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.693A pdb=" N LYS R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.887A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.599A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 341 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.174A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.666A 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: 3.834A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.114A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.758A 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: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.241A 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: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.633A 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: 3.647A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.957A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1600 1.33 - 1.45: 1437 1.45 - 1.57: 3720 1.57 - 1.69: 5 1.69 - 1.82: 51 Bond restraints: 6813 Sorted by residual: bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.70e+00 bond pdb=" N ARG B 129 " pdb=" CA ARG B 129 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.06e+00 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.22e-02 6.72e+03 7.88e+00 bond pdb=" N VAL G 16 " pdb=" CA VAL G 16 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.83e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.66e+00 ... (remaining 6808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9010 2.12 - 4.25: 278 4.25 - 6.37: 28 6.37 - 8.49: 10 8.49 - 10.61: 4 Bond angle restraints: 9330 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.91 7.37 1.09e+00 8.42e-01 4.57e+01 angle pdb=" N SER G 8 " pdb=" CA SER G 8 " pdb=" C SER G 8 " ideal model delta sigma weight residual 112.38 104.62 7.76 1.22e+00 6.72e-01 4.05e+01 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 111.28 104.82 6.46 1.09e+00 8.42e-01 3.51e+01 angle pdb=" N HIS R 269 " pdb=" CA HIS R 269 " pdb=" C HIS R 269 " ideal model delta sigma weight residual 113.88 106.94 6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N ASP A 11 " pdb=" CA ASP A 11 " pdb=" C ASP A 11 " ideal model delta sigma weight residual 111.28 106.23 5.05 1.09e+00 8.42e-01 2.15e+01 ... (remaining 9325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.92: 3808 28.92 - 57.85: 119 57.85 - 86.77: 6 86.77 - 115.69: 0 115.69 - 144.61: 2 Dihedral angle restraints: 3935 sinusoidal: 1250 harmonic: 2685 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 155.75 -62.75 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -146.12 -144.61 1 2.00e+01 2.50e-03 4.36e+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 -34.69 139.28 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 817 0.046 - 0.093: 202 0.093 - 0.139: 79 0.139 - 0.186: 17 0.186 - 0.232: 7 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA GLN A 12 " pdb=" N GLN A 12 " pdb=" C GLN A 12 " pdb=" CB GLN A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE R 38 " pdb=" N ILE R 38 " pdb=" C ILE R 38 " pdb=" CB ILE R 38 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL R 33 " pdb=" N VAL R 33 " pdb=" C VAL R 33 " pdb=" CB VAL R 33 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1119 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 239 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG R 239 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG R 239 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE R 240 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 12 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C GLN A 12 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 12 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 13 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 19 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLN A 19 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN A 19 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 20 " 0.012 2.00e-02 2.50e+03 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 29 2.54 - 3.13: 4958 3.13 - 3.72: 9727 3.72 - 4.31: 12697 4.31 - 4.90: 22385 Nonbonded interactions: 49796 Sorted by model distance: nonbonded pdb=" NH1 ARG A 231 " pdb=" O ARG A 232 " model vdw 1.950 3.120 nonbonded pdb=" OD1 ASN B 295 " pdb=" NH2 ARG B 304 " model vdw 2.200 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.214 3.040 nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 2.260 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.268 3.120 ... (remaining 49791 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=0.49 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: 1.900 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.970 Find NCS groups from input model: 0.070 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.055 6813 Z= 0.323 Angle : 0.787 10.613 9330 Z= 0.521 Chirality : 0.051 0.232 1122 Planarity : 0.004 0.039 1169 Dihedral : 13.749 144.614 2187 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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 (0.29), residues: 908 helix: 1.93 (0.27), residues: 412 sheet: 0.44 (0.41), residues: 172 loop : -0.89 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE B 234 TYR 0.015 0.001 TYR A 339 ARG 0.008 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1992 time to fit residues: 32.3997 Evaluate side-chains 86 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN R 93 HIS R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093776 restraints weight = 30804.898| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.50 r_work: 0.2930 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6813 Z= 0.212 Angle : 0.507 6.141 9330 Z= 0.275 Chirality : 0.042 0.133 1122 Planarity : 0.003 0.039 1169 Dihedral : 7.915 142.200 1010 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.68 % Allowed : 9.73 % Favored : 88.59 % 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: 1.34 (0.29), residues: 908 helix: 2.30 (0.27), residues: 410 sheet: 0.45 (0.40), residues: 181 loop : -0.73 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.010 0.001 HIS R 93 PHE 0.010 0.001 PHE R 217 TYR 0.015 0.001 TYR A 311 ARG 0.006 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7258 (mtm) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.1744 time to fit residues: 22.8106 Evaluate side-chains 92 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093917 restraints weight = 35813.492| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.83 r_work: 0.2925 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6813 Z= 0.168 Angle : 0.462 6.576 9330 Z= 0.251 Chirality : 0.041 0.151 1122 Planarity : 0.003 0.038 1169 Dihedral : 7.634 140.158 1010 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.18 % Allowed : 10.91 % Favored : 86.91 % 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: 908 helix: 2.52 (0.27), residues: 410 sheet: 0.50 (0.41), residues: 174 loop : -0.82 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.008 0.001 HIS R 93 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8794 (t0) cc_final: 0.8521 (t0) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.1690 time to fit residues: 22.5694 Evaluate side-chains 93 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093966 restraints weight = 39393.969| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.15 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6813 Z= 0.162 Angle : 0.456 6.929 9330 Z= 0.248 Chirality : 0.041 0.177 1122 Planarity : 0.003 0.038 1169 Dihedral : 7.519 140.323 1010 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.68 % Allowed : 11.24 % Favored : 86.07 % 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: 1.56 (0.29), residues: 908 helix: 2.59 (0.27), residues: 410 sheet: 0.61 (0.41), residues: 174 loop : -0.81 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.004 0.001 HIS R 93 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8592 (t0) cc_final: 0.8301 (t0) REVERT: B 259 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7699 (pt0) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 0.1580 time to fit residues: 22.6712 Evaluate side-chains 97 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091369 restraints weight = 32252.500| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.47 r_work: 0.2899 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6813 Z= 0.254 Angle : 0.497 7.143 9330 Z= 0.269 Chirality : 0.042 0.180 1122 Planarity : 0.003 0.041 1169 Dihedral : 7.550 140.344 1010 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.52 % Allowed : 12.25 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 908 helix: 2.53 (0.27), residues: 410 sheet: 0.45 (0.40), residues: 180 loop : -0.84 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.007 0.001 HIS R 93 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.006 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 259 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: G 48 ASP cc_start: 0.8797 (p0) cc_final: 0.8594 (p0) outliers start: 21 outliers final: 19 residues processed: 95 average time/residue: 0.1519 time to fit residues: 20.8446 Evaluate side-chains 99 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090867 restraints weight = 34832.990| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.64 r_work: 0.2877 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6813 Z= 0.267 Angle : 0.503 7.214 9330 Z= 0.273 Chirality : 0.042 0.139 1122 Planarity : 0.003 0.042 1169 Dihedral : 7.594 140.942 1010 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.36 % Allowed : 13.93 % Favored : 82.72 % 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: 1.33 (0.29), residues: 908 helix: 2.41 (0.27), residues: 411 sheet: 0.37 (0.40), residues: 180 loop : -0.88 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.015 0.001 TYR A 358 ARG 0.006 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 THR cc_start: 0.8624 (t) cc_final: 0.8279 (p) REVERT: B 197 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7531 (mmp-170) REVERT: B 259 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7931 (pt0) outliers start: 20 outliers final: 19 residues processed: 93 average time/residue: 0.1553 time to fit residues: 21.1379 Evaluate side-chains 94 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090434 restraints weight = 34269.592| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.61 r_work: 0.2872 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6813 Z= 0.262 Angle : 0.505 7.231 9330 Z= 0.274 Chirality : 0.042 0.184 1122 Planarity : 0.003 0.054 1169 Dihedral : 7.617 141.485 1010 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.19 % Allowed : 13.93 % Favored : 81.88 % 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: 1.26 (0.29), residues: 908 helix: 2.40 (0.27), residues: 410 sheet: 0.24 (0.40), residues: 182 loop : -0.91 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.008 0.001 HIS R 93 PHE 0.013 0.001 PHE B 241 TYR 0.014 0.001 TYR A 358 ARG 0.006 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 THR cc_start: 0.8548 (t) cc_final: 0.8243 (p) REVERT: B 197 ARG cc_start: 0.7774 (tpp-160) cc_final: 0.7558 (mmp-170) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8221 (t80) REVERT: B 237 ASN cc_start: 0.8812 (t0) cc_final: 0.8408 (t0) REVERT: B 259 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: R 294 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8614 (mp) outliers start: 25 outliers final: 20 residues processed: 94 average time/residue: 0.1452 time to fit residues: 19.7612 Evaluate side-chains 95 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093017 restraints weight = 36214.972| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.77 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6813 Z= 0.126 Angle : 0.448 7.236 9330 Z= 0.244 Chirality : 0.040 0.147 1122 Planarity : 0.003 0.061 1169 Dihedral : 7.474 142.584 1010 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.68 % Allowed : 15.77 % Favored : 81.54 % 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: 1.45 (0.29), residues: 908 helix: 2.57 (0.27), residues: 410 sheet: 0.38 (0.40), residues: 180 loop : -0.86 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.005 0.001 HIS R 93 PHE 0.020 0.001 PHE A 212 TYR 0.011 0.001 TYR A 358 ARG 0.007 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: B 197 ARG cc_start: 0.7463 (tpp-160) cc_final: 0.7200 (mmp-170) REVERT: B 234 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7999 (t80) REVERT: B 237 ASN cc_start: 0.8525 (t0) cc_final: 0.8119 (t0) REVERT: B 259 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7676 (pt0) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.1614 time to fit residues: 22.6228 Evaluate side-chains 95 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094620 restraints weight = 29266.179| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.35 r_work: 0.2947 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6813 Z= 0.119 Angle : 0.447 7.275 9330 Z= 0.243 Chirality : 0.040 0.142 1122 Planarity : 0.004 0.076 1169 Dihedral : 7.402 143.112 1010 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.35 % Allowed : 16.95 % Favored : 80.70 % 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: 1.54 (0.29), residues: 908 helix: 2.67 (0.27), residues: 404 sheet: 0.45 (0.39), residues: 180 loop : -0.80 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR A 358 ARG 0.007 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: B 197 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7525 (mmp-170) REVERT: B 234 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8013 (t80) REVERT: B 237 ASN cc_start: 0.8727 (t0) cc_final: 0.8331 (t0) REVERT: B 259 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: R 40 MET cc_start: 0.7702 (mtm) cc_final: 0.7371 (mtt) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.1504 time to fit residues: 21.6862 Evaluate side-chains 98 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094122 restraints weight = 30264.064| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.39 r_work: 0.2938 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6813 Z= 0.144 Angle : 0.455 7.299 9330 Z= 0.247 Chirality : 0.040 0.133 1122 Planarity : 0.004 0.084 1169 Dihedral : 7.380 143.368 1010 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.35 % Allowed : 17.28 % Favored : 80.37 % 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: 1.52 (0.29), residues: 908 helix: 2.65 (0.27), residues: 404 sheet: 0.42 (0.39), residues: 180 loop : -0.81 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 277 HIS 0.013 0.001 HIS R 93 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 311 ARG 0.007 0.000 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: B 234 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 237 ASN cc_start: 0.8751 (t0) cc_final: 0.8350 (t0) REVERT: B 259 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: R 40 MET cc_start: 0.7693 (mtm) cc_final: 0.7394 (mtt) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.1563 time to fit residues: 22.0091 Evaluate side-chains 94 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.0060 chunk 6 optimal weight: 0.0470 chunk 40 optimal weight: 0.0470 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094887 restraints weight = 32990.780| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.57 r_work: 0.2944 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6813 Z= 0.115 Angle : 0.440 7.307 9330 Z= 0.239 Chirality : 0.040 0.129 1122 Planarity : 0.004 0.087 1169 Dihedral : 7.330 143.545 1010 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.35 % Allowed : 17.11 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.29), residues: 908 helix: 2.69 (0.27), residues: 404 sheet: 0.45 (0.39), residues: 180 loop : -0.78 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.013 0.001 HIS R 93 PHE 0.010 0.001 PHE B 241 TYR 0.010 0.001 TYR A 311 ARG 0.007 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.76 seconds wall clock time: 61 minutes 53.18 seconds (3713.18 seconds total)