Starting phenix.real_space_refine on Fri Jul 3 16:33:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpn_22416/07_2026/7jpn_22416.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 9562 2.51 5 N 2583 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3194 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2728 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2637 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2291 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1414 Classifications: {'peptide': 174} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1369 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1084 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 15040 At special positions: 0 Unit cell: (93.632, 149.644, 134.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 2 11.99 O 2809 8.00 N 2583 7.00 C 9562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.01 Conformation dependent library (CDL) restraints added in 647.6 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 43.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.769A pdb=" N ILE A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.535A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 219 through 231 removed outlier: 3.532A pdb=" N VAL A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.924A pdb=" N PHE A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.587A pdb=" N ARG A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 330 through 355 Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.391A pdb=" N TYR A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.702A pdb=" N HIS A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.508A pdb=" N MET B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.852A pdb=" N GLU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Proline residue: B 262 - end of helix No H-bonds generated for 'chain 'B' and resid 256 through 264' Processing helix chain 'B' and resid 265 through 266 No H-bonds generated for 'chain 'B' and resid 265 through 266' Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.649A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.163A pdb=" N SER B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.917A pdb=" N MET B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.813A pdb=" N SER C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.618A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 105 through 115 removed outlier: 4.531A pdb=" N ILE D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 135 removed outlier: 4.065A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 Processing helix chain 'D' and resid 188 through 191 removed outlier: 3.586A pdb=" N ALA D 191 " --> pdb=" O GLY D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 206 through 211 removed outlier: 4.544A pdb=" N ASP D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.639A pdb=" N ASP D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 280 Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.946A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.760A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 Processing helix chain 'E' and resid 122 through 149 removed outlier: 4.012A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.505A pdb=" N THR E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.882A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 167 removed outlier: 3.729A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 38 through 48 removed outlier: 3.543A pdb=" N VAL G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 68 through 86 removed outlier: 3.992A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.636A pdb=" N ALA G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 115 removed outlier: 4.004A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 147 removed outlier: 3.647A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N GLY G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 201 Processing helix chain 'H' and resid 202 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.813A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.336A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 32 removed outlier: 4.345A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 139 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.802A pdb=" N GLU B 75 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.077A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.343A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN C 344 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.679A pdb=" N GLU C 36 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 44 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TRP C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 61 removed outlier: 3.807A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 104 removed outlier: 3.642A pdb=" N GLU C 126 " --> pdb=" O TRP C 131 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP C 131 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.976A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 205 through 210 removed outlier: 3.502A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 247 through 252 removed outlier: 6.619A pdb=" N LEU C 269 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 33 through 37 removed outlier: 3.757A pdb=" N VAL D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 94 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AC3, first strand: chain 'E' and resid 14 through 16 removed outlier: 4.221A pdb=" N LYS E 14 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 732 hydrogen bonds defined for protein. 2019 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: 2.73 Time building geometry restraints manager: 1.42 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: 3151 1.33 - 1.45: 3499 1.45 - 1.57: 8594 1.57 - 1.69: 10 1.69 - 1.81: 119 Bond restraints: 15373 Sorted by residual: bond pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.30e-03 1.16e+04 9.77e+00 bond pdb=" N GLU H 214 " pdb=" CA GLU H 214 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 9.02e+00 bond pdb=" N ILE H 212 " pdb=" CA ILE H 212 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.33e+00 bond pdb=" N HIS A 410 " pdb=" CA HIS A 410 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.22e-02 6.72e+03 7.72e+00 bond pdb=" N LYS H 203 " pdb=" CA LYS H 203 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 ... (remaining 15368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 20431 2.08 - 4.16: 327 4.16 - 6.25: 38 6.25 - 8.33: 7 8.33 - 10.41: 4 Bond angle restraints: 20807 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" CA ASN A 411 " pdb=" CB ASN A 411 " ideal model delta sigma weight residual 110.17 118.22 -8.05 1.11e+00 8.12e-01 5.26e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 107.78 5.42 9.60e-01 1.09e+00 3.19e+01 angle pdb=" C TYR A 391 " pdb=" CA TYR A 391 " pdb=" CB TYR A 391 " ideal model delta sigma weight residual 110.63 121.04 -10.41 1.85e+00 2.92e-01 3.17e+01 angle pdb=" C ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta sigma weight residual 110.85 120.14 -9.29 1.70e+00 3.46e-01 2.98e+01 angle pdb=" C ARG B 6 " pdb=" CA ARG B 6 " pdb=" CB ARG B 6 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 ... (remaining 20802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8266 17.70 - 35.41: 774 35.41 - 53.11: 152 53.11 - 70.81: 23 70.81 - 88.52: 11 Dihedral angle restraints: 9226 sinusoidal: 3752 harmonic: 5474 Sorted by residual: dihedral pdb=" C ASN H 198 " pdb=" N ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta harmonic sigma weight residual -122.60 -138.83 16.23 0 2.50e+00 1.60e-01 4.21e+01 dihedral pdb=" N ASN H 198 " pdb=" C ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta harmonic sigma weight residual 122.80 136.15 -13.35 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C TYR A 391 " pdb=" N TYR A 391 " pdb=" CA TYR A 391 " pdb=" CB TYR A 391 " ideal model delta harmonic sigma weight residual -122.60 -133.23 10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 9223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2221 0.113 - 0.225: 54 0.225 - 0.338: 4 0.338 - 0.450: 1 0.450 - 0.563: 1 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CA ASN H 198 " pdb=" N ASN H 198 " pdb=" C ASN H 198 " pdb=" CB ASN H 198 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" CA ASP H 217 " pdb=" N ASP H 217 " pdb=" C ASP H 217 " pdb=" CB ASP H 217 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE E 16 " pdb=" CA ILE E 16 " pdb=" CG1 ILE E 16 " pdb=" CG2 ILE E 16 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2278 not shown) Planarity restraints: 2674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 224 " 0.037 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP H 224 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP H 224 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 224 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP H 224 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 224 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 224 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 224 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 224 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 224 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 386 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C SER A 386 " 0.035 2.00e-02 2.50e+03 pdb=" O SER A 386 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 387 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 151 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO C 152 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.027 5.00e-02 4.00e+02 ... (remaining 2671 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 89 2.52 - 3.11: 10992 3.11 - 3.71: 23650 3.71 - 4.30: 34048 4.30 - 4.90: 57017 Nonbonded interactions: 125796 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ATP A 502 " model vdw 1.919 2.170 nonbonded pdb=" NH1 ARG B 214 " pdb=" OE2 GLU B 218 " model vdw 2.104 3.120 nonbonded pdb=" OG SER C 170 " pdb=" O PRO C 190 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR A 233 " pdb=" OE1 GLU A 241 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP B 158 " pdb="MG MG B 501 " model vdw 2.198 2.170 ... (remaining 125791 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: 2.190 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15373 Z= 0.198 Angle : 0.632 10.409 20807 Z= 0.371 Chirality : 0.049 0.563 2281 Planarity : 0.004 0.048 2674 Dihedral : 14.272 88.518 5694 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.55 % Allowed : 0.92 % Favored : 98.52 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1863 helix: 1.14 (0.20), residues: 694 sheet: -0.36 (0.27), residues: 361 loop : -0.01 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 350 TYR 0.029 0.002 TYR A 125 PHE 0.029 0.002 PHE A 283 TRP 0.037 0.002 TRP H 224 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (15373) covalent geometry : angle 0.63179 / 0.37 (20807) hydrogen bonds : bond 0.12316 / 8.24 ( 728) hydrogen bonds : angle 5.74829 / 4.04 ( 2019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 489 time to evaluate : 0.561 Fit side-chains REVERT: A 93 MET cc_start: 0.7210 (tpp) cc_final: 0.7009 (tpp) REVERT: A 188 SER cc_start: 0.8346 (p) cc_final: 0.8084 (m) REVERT: A 205 GLN cc_start: 0.7583 (tt0) cc_final: 0.7332 (tt0) REVERT: A 237 ASP cc_start: 0.6549 (t70) cc_final: 0.6281 (t70) REVERT: A 255 GLN cc_start: 0.8618 (mp10) cc_final: 0.8412 (mm-40) REVERT: A 274 GLU cc_start: 0.6665 (pm20) cc_final: 0.6113 (pm20) REVERT: A 292 PHE cc_start: 0.7624 (t80) cc_final: 0.7048 (t80) REVERT: A 333 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7198 (tpp80) REVERT: A 338 ASP cc_start: 0.6751 (m-30) cc_final: 0.6549 (m-30) REVERT: A 344 ASP cc_start: 0.7409 (m-30) cc_final: 0.7184 (m-30) REVERT: A 368 ILE cc_start: 0.8144 (mm) cc_final: 0.7930 (mm) REVERT: B 74 MET cc_start: 0.0246 (mmp) cc_final: -0.0024 (mmp) REVERT: B 85 MET cc_start: 0.7601 (mmp) cc_final: 0.7196 (mmp) REVERT: B 115 ASN cc_start: 0.7828 (t0) cc_final: 0.7571 (t0) REVERT: B 127 MET cc_start: 0.7141 (mmp) cc_final: 0.6871 (mmp) REVERT: B 140 ILE cc_start: 0.8018 (mt) cc_final: 0.7804 (mt) REVERT: B 257 GLU cc_start: 0.7223 (mp0) cc_final: 0.6930 (mp0) REVERT: B 260 GLU cc_start: 0.6917 (mp0) cc_final: 0.6574 (mp0) REVERT: C 64 SER cc_start: 0.8503 (m) cc_final: 0.8267 (m) REVERT: C 92 ILE cc_start: 0.8133 (pt) cc_final: 0.7314 (pt) REVERT: C 102 VAL cc_start: 0.7970 (p) cc_final: 0.7558 (t) REVERT: C 178 GLU cc_start: 0.7051 (pm20) cc_final: 0.6778 (pm20) REVERT: C 225 THR cc_start: 0.8242 (p) cc_final: 0.8020 (p) REVERT: D 5 GLU cc_start: 0.6990 (pm20) cc_final: 0.6630 (pm20) REVERT: D 65 LYS cc_start: 0.7891 (mttp) cc_final: 0.7639 (mttp) REVERT: D 74 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6690 (tm-30) REVERT: D 106 LYS cc_start: 0.8187 (mppt) cc_final: 0.7929 (mppt) REVERT: D 119 ASN cc_start: 0.8014 (m110) cc_final: 0.7696 (m-40) REVERT: D 186 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7805 (ttmm) REVERT: D 204 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6751 (mm-30) REVERT: E 14 LYS cc_start: 0.7766 (mptt) cc_final: 0.7514 (mptt) REVERT: E 63 GLU cc_start: 0.7579 (mp0) cc_final: 0.7179 (mp0) REVERT: E 80 LYS cc_start: 0.7488 (mttp) cc_final: 0.7199 (mttp) REVERT: E 88 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7938 (tmmt) REVERT: F 39 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6836 (mm-30) REVERT: F 45 GLU cc_start: 0.7776 (pm20) cc_final: 0.7473 (pm20) REVERT: F 141 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6358 (mm-30) REVERT: F 163 GLU cc_start: 0.6999 (tp30) cc_final: 0.6430 (tp30) REVERT: F 167 ASN cc_start: 0.7235 (m110) cc_final: 0.7016 (m-40) REVERT: G 107 MET cc_start: 0.7442 (tpp) cc_final: 0.7070 (tpp) outliers start: 9 outliers final: 3 residues processed: 497 average time/residue: 0.1667 time to fit residues: 112.8738 Evaluate side-chains 478 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 475 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 366 GLN A 373 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN C 30 HIS D 245 HIS F 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118386 restraints weight = 21706.159| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.12 r_work: 0.3315 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15373 Z= 0.166 Angle : 0.542 8.268 20807 Z= 0.287 Chirality : 0.045 0.206 2281 Planarity : 0.004 0.053 2674 Dihedral : 4.985 58.090 2055 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.11 % Allowed : 8.73 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1863 helix: 1.52 (0.20), residues: 687 sheet: -0.22 (0.27), residues: 356 loop : 0.00 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 161 TYR 0.022 0.002 TYR A 125 PHE 0.022 0.002 PHE B 340 TRP 0.023 0.002 TRP E 160 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (15373) covalent geometry : angle 0.54213 / 0.29 (20807) hydrogen bonds : bond 0.03925 / 2.56 ( 728) hydrogen bonds : angle 4.82030 / 3.39 ( 2019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 481 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.8594 (mm) cc_final: 0.8274 (mm) REVERT: A 79 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: A 85 ASP cc_start: 0.7309 (t0) cc_final: 0.7079 (t0) REVERT: A 93 MET cc_start: 0.8054 (tpp) cc_final: 0.7639 (tpp) REVERT: A 123 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7827 (mtt-85) REVERT: A 128 GLU cc_start: 0.8317 (tt0) cc_final: 0.7849 (tt0) REVERT: A 188 SER cc_start: 0.8619 (p) cc_final: 0.8409 (m) REVERT: A 221 LEU cc_start: 0.8433 (tp) cc_final: 0.8204 (tp) REVERT: A 229 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 255 GLN cc_start: 0.8717 (mp10) cc_final: 0.8447 (mm-40) REVERT: A 292 PHE cc_start: 0.7773 (t80) cc_final: 0.7083 (t80) REVERT: A 333 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8262 (ttm-80) REVERT: A 338 ASP cc_start: 0.7374 (m-30) cc_final: 0.7082 (m-30) REVERT: A 344 ASP cc_start: 0.7912 (m-30) cc_final: 0.7649 (m-30) REVERT: A 386 SER cc_start: 0.8608 (t) cc_final: 0.8380 (t) REVERT: A 389 GLU cc_start: 0.8035 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 74 MET cc_start: 0.0388 (mmp) cc_final: -0.0007 (mmp) REVERT: B 85 MET cc_start: 0.8001 (mmp) cc_final: 0.7547 (mmp) REVERT: B 115 ASN cc_start: 0.8160 (t0) cc_final: 0.7890 (t0) REVERT: B 127 MET cc_start: 0.7732 (mmp) cc_final: 0.7441 (mmp) REVERT: B 140 ILE cc_start: 0.8178 (mt) cc_final: 0.7976 (mt) REVERT: B 145 THR cc_start: 0.8478 (m) cc_final: 0.8209 (m) REVERT: B 171 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 214 ARG cc_start: 0.8207 (ttp80) cc_final: 0.8005 (ttp80) REVERT: B 257 GLU cc_start: 0.7945 (mp0) cc_final: 0.7667 (mp0) REVERT: B 260 GLU cc_start: 0.7612 (mp0) cc_final: 0.6997 (mp0) REVERT: C 58 ILE cc_start: 0.8438 (mt) cc_final: 0.8050 (tt) REVERT: C 92 ILE cc_start: 0.8364 (pt) cc_final: 0.8138 (pt) REVERT: C 195 MET cc_start: 0.8439 (mmm) cc_final: 0.8004 (mmm) REVERT: C 326 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8226 (mmmt) REVERT: D 5 GLU cc_start: 0.7540 (pm20) cc_final: 0.7140 (pm20) REVERT: D 65 LYS cc_start: 0.8341 (mttp) cc_final: 0.8093 (mttp) REVERT: D 74 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7492 (tm-30) REVERT: D 106 LYS cc_start: 0.8528 (mppt) cc_final: 0.8142 (mppt) REVERT: D 115 MET cc_start: 0.7603 (mtm) cc_final: 0.7120 (mtt) REVERT: D 119 ASN cc_start: 0.8613 (m110) cc_final: 0.8216 (m-40) REVERT: D 186 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7793 (ttmm) REVERT: D 204 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7137 (mm-30) REVERT: D 230 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8082 (ptp90) REVERT: E 14 LYS cc_start: 0.7833 (mptt) cc_final: 0.7549 (mptt) REVERT: E 63 GLU cc_start: 0.8160 (mp0) cc_final: 0.7819 (mp0) REVERT: E 80 LYS cc_start: 0.7841 (mttp) cc_final: 0.7585 (mttp) REVERT: E 88 LYS cc_start: 0.8351 (tmmt) cc_final: 0.7985 (tmmt) REVERT: F 39 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7500 (mm-30) REVERT: F 45 GLU cc_start: 0.8254 (pm20) cc_final: 0.8014 (pm20) REVERT: F 141 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7216 (mm-30) REVERT: F 163 GLU cc_start: 0.7698 (tp30) cc_final: 0.6960 (tp30) REVERT: F 167 ASN cc_start: 0.7704 (m110) cc_final: 0.7428 (m-40) REVERT: H 222 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7154 (mm-30) outliers start: 18 outliers final: 11 residues processed: 488 average time/residue: 0.1654 time to fit residues: 109.6558 Evaluate side-chains 485 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 474 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117356 restraints weight = 21941.751| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.12 r_work: 0.3307 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15373 Z= 0.168 Angle : 0.526 9.228 20807 Z= 0.277 Chirality : 0.045 0.172 2281 Planarity : 0.004 0.055 2674 Dihedral : 4.824 56.241 2053 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.29 % Allowed : 11.68 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1863 helix: 1.56 (0.20), residues: 688 sheet: -0.15 (0.28), residues: 351 loop : -0.03 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 161 TYR 0.031 0.002 TYR B 298 PHE 0.021 0.002 PHE A 276 TRP 0.013 0.001 TRP H 224 HIS 0.008 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15373) covalent geometry : angle 0.52600 / 0.28 (20807) hydrogen bonds : bond 0.03762 / 2.46 ( 728) hydrogen bonds : angle 4.69937 / 3.30 ( 2019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 485 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.8571 (mm) cc_final: 0.8270 (mm) REVERT: A 79 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7296 (mtm-85) REVERT: A 93 MET cc_start: 0.8101 (tpp) cc_final: 0.7720 (tmm) REVERT: A 128 GLU cc_start: 0.8274 (tt0) cc_final: 0.7740 (tt0) REVERT: A 188 SER cc_start: 0.8607 (p) cc_final: 0.8404 (m) REVERT: A 255 GLN cc_start: 0.8725 (mp10) cc_final: 0.8393 (mm-40) REVERT: A 267 PHE cc_start: 0.8033 (p90) cc_final: 0.7602 (p90) REVERT: A 292 PHE cc_start: 0.7837 (t80) cc_final: 0.7130 (t80) REVERT: A 338 ASP cc_start: 0.7402 (m-30) cc_final: 0.7126 (m-30) REVERT: A 373 GLN cc_start: 0.8249 (tt0) cc_final: 0.8042 (tt0) REVERT: A 386 SER cc_start: 0.8648 (t) cc_final: 0.8427 (t) REVERT: A 406 SER cc_start: 0.8625 (m) cc_final: 0.8401 (p) REVERT: B 74 MET cc_start: 0.0311 (mmp) cc_final: -0.0159 (mmp) REVERT: B 85 MET cc_start: 0.8022 (mmp) cc_final: 0.7507 (mmp) REVERT: B 115 ASN cc_start: 0.8197 (t0) cc_final: 0.7956 (t0) REVERT: B 127 MET cc_start: 0.7664 (mmp) cc_final: 0.7399 (mmp) REVERT: B 140 ILE cc_start: 0.8187 (mt) cc_final: 0.7978 (mt) REVERT: B 171 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 257 GLU cc_start: 0.7914 (mp0) cc_final: 0.7653 (mp0) REVERT: B 260 GLU cc_start: 0.7727 (mp0) cc_final: 0.7057 (mp0) REVERT: B 340 PHE cc_start: 0.8144 (t80) cc_final: 0.7794 (t80) REVERT: B 346 ASP cc_start: 0.7393 (p0) cc_final: 0.7010 (p0) REVERT: B 365 MET cc_start: 0.5093 (ppp) cc_final: 0.4678 (ppp) REVERT: C 110 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8186 (pttm) REVERT: C 195 MET cc_start: 0.8462 (mmm) cc_final: 0.7998 (mmm) REVERT: C 326 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8338 (mmmt) REVERT: D 65 LYS cc_start: 0.8331 (mttp) cc_final: 0.8078 (mttp) REVERT: D 74 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 106 LYS cc_start: 0.8581 (mppt) cc_final: 0.8168 (mppt) REVERT: D 115 MET cc_start: 0.7744 (mtm) cc_final: 0.7198 (mtm) REVERT: D 119 ASN cc_start: 0.8662 (m110) cc_final: 0.8256 (m-40) REVERT: D 141 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8345 (ptp-110) REVERT: D 166 SER cc_start: 0.8258 (m) cc_final: 0.7962 (t) REVERT: D 186 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7750 (ttmm) REVERT: D 204 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7204 (mm-30) REVERT: D 266 MET cc_start: 0.8232 (mtt) cc_final: 0.7878 (mtp) REVERT: E 14 LYS cc_start: 0.7813 (mptt) cc_final: 0.7538 (mptt) REVERT: E 19 MET cc_start: 0.7179 (mmm) cc_final: 0.6821 (tpt) REVERT: E 88 LYS cc_start: 0.8353 (tmmt) cc_final: 0.7970 (tmmt) REVERT: E 129 MET cc_start: 0.7700 (ttm) cc_final: 0.7489 (ttm) REVERT: F 39 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7554 (mm-30) REVERT: F 141 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7181 (mm-30) REVERT: F 163 GLU cc_start: 0.7734 (tp30) cc_final: 0.6995 (tp30) REVERT: F 167 ASN cc_start: 0.7724 (m110) cc_final: 0.7440 (m-40) outliers start: 21 outliers final: 17 residues processed: 491 average time/residue: 0.1611 time to fit residues: 107.6925 Evaluate side-chains 497 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 480 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 134 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 HIS F 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119399 restraints weight = 21825.286| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.14 r_work: 0.3331 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15373 Z= 0.126 Angle : 0.510 9.665 20807 Z= 0.267 Chirality : 0.044 0.144 2281 Planarity : 0.004 0.053 2674 Dihedral : 4.674 55.563 2053 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.48 % Allowed : 13.71 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1863 helix: 1.61 (0.20), residues: 693 sheet: -0.13 (0.28), residues: 353 loop : 0.06 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 281 TYR 0.031 0.001 TYR E 74 PHE 0.026 0.002 PHE B 355 TRP 0.012 0.001 TRP C 131 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15373) covalent geometry : angle 0.50963 / 0.27 (20807) hydrogen bonds : bond 0.03451 / 2.27 ( 728) hydrogen bonds : angle 4.58083 / 3.22 ( 2019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 482 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8647 (m-80) cc_final: 0.8417 (m-80) REVERT: A 79 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7218 (mtm-85) REVERT: A 93 MET cc_start: 0.8061 (tpp) cc_final: 0.7788 (mmm) REVERT: A 128 GLU cc_start: 0.8236 (tt0) cc_final: 0.7839 (tt0) REVERT: A 230 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7817 (mtp-110) REVERT: A 250 SER cc_start: 0.8909 (t) cc_final: 0.8617 (t) REVERT: A 255 GLN cc_start: 0.8706 (mp10) cc_final: 0.8385 (mm-40) REVERT: A 267 PHE cc_start: 0.8061 (p90) cc_final: 0.7570 (p90) REVERT: A 292 PHE cc_start: 0.7815 (t80) cc_final: 0.7076 (t80) REVERT: A 338 ASP cc_start: 0.7432 (m-30) cc_final: 0.7158 (m-30) REVERT: A 386 SER cc_start: 0.8586 (t) cc_final: 0.8321 (t) REVERT: A 406 SER cc_start: 0.8614 (m) cc_final: 0.8351 (p) REVERT: B 74 MET cc_start: 0.0107 (mmp) cc_final: -0.0233 (mmp) REVERT: B 85 MET cc_start: 0.7979 (mmp) cc_final: 0.7452 (mmp) REVERT: B 108 LEU cc_start: 0.8640 (tt) cc_final: 0.8401 (tp) REVERT: B 115 ASN cc_start: 0.8185 (t0) cc_final: 0.7967 (t0) REVERT: B 122 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7798 (tmtt) REVERT: B 127 MET cc_start: 0.7690 (mmp) cc_final: 0.7443 (mmp) REVERT: B 171 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 214 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7985 (ttp80) REVERT: B 242 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 257 GLU cc_start: 0.7890 (mp0) cc_final: 0.7644 (mp0) REVERT: B 260 GLU cc_start: 0.7754 (mp0) cc_final: 0.7108 (mp0) REVERT: B 346 ASP cc_start: 0.7321 (p0) cc_final: 0.7116 (p0) REVERT: B 365 MET cc_start: 0.5020 (ppp) cc_final: 0.4525 (ppp) REVERT: C 58 ILE cc_start: 0.8398 (mt) cc_final: 0.8073 (tt) REVERT: C 79 TRP cc_start: 0.8935 (m100) cc_final: 0.8557 (m100) REVERT: C 110 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8287 (pttm) REVERT: C 195 MET cc_start: 0.8469 (mmm) cc_final: 0.8059 (mmm) REVERT: C 326 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8330 (mmmt) REVERT: D 74 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 106 LYS cc_start: 0.8601 (mppt) cc_final: 0.8172 (mppt) REVERT: D 110 VAL cc_start: 0.7949 (t) cc_final: 0.7645 (p) REVERT: D 115 MET cc_start: 0.7791 (mtm) cc_final: 0.7206 (mtm) REVERT: D 119 ASN cc_start: 0.8678 (m110) cc_final: 0.8255 (m-40) REVERT: D 166 SER cc_start: 0.8305 (m) cc_final: 0.7996 (t) REVERT: D 186 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7727 (ttmm) REVERT: D 204 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7151 (mm-30) REVERT: D 266 MET cc_start: 0.8250 (mtt) cc_final: 0.7914 (mtp) REVERT: E 14 LYS cc_start: 0.7824 (mptt) cc_final: 0.7524 (mptt) REVERT: E 80 LYS cc_start: 0.7836 (mttp) cc_final: 0.7466 (mttp) REVERT: E 88 LYS cc_start: 0.8373 (tmmt) cc_final: 0.7992 (tmmt) REVERT: E 129 MET cc_start: 0.7817 (ttm) cc_final: 0.7430 (ttm) REVERT: F 39 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 70 VAL cc_start: 0.8687 (p) cc_final: 0.8416 (t) REVERT: F 163 GLU cc_start: 0.7715 (tp30) cc_final: 0.7009 (tp30) REVERT: F 167 ASN cc_start: 0.7689 (m110) cc_final: 0.7391 (m-40) REVERT: H 222 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7301 (tm-30) outliers start: 24 outliers final: 14 residues processed: 491 average time/residue: 0.1577 time to fit residues: 105.7562 Evaluate side-chains 483 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 469 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118472 restraints weight = 21779.939| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.11 r_work: 0.3318 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15373 Z= 0.158 Angle : 0.516 10.224 20807 Z= 0.272 Chirality : 0.045 0.305 2281 Planarity : 0.004 0.052 2674 Dihedral : 4.665 55.331 2053 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.03 % Allowed : 14.63 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1863 helix: 1.61 (0.20), residues: 692 sheet: -0.20 (0.28), residues: 357 loop : 0.08 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 281 TYR 0.034 0.001 TYR E 74 PHE 0.022 0.002 PHE A 276 TRP 0.013 0.001 TRP H 224 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15373) covalent geometry : angle 0.51567 / 0.27 (20807) hydrogen bonds : bond 0.03549 / 2.33 ( 728) hydrogen bonds : angle 4.55299 / 3.21 ( 2019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 481 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: A 93 MET cc_start: 0.8123 (tpp) cc_final: 0.7713 (mmm) REVERT: A 114 GLU cc_start: 0.8147 (pt0) cc_final: 0.7785 (pt0) REVERT: A 123 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7890 (mtt-85) REVERT: A 128 GLU cc_start: 0.8218 (tt0) cc_final: 0.7813 (tt0) REVERT: A 161 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7892 (mtm180) REVERT: A 229 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 230 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7792 (mtp-110) REVERT: A 255 GLN cc_start: 0.8699 (mp10) cc_final: 0.8370 (mm-40) REVERT: A 267 PHE cc_start: 0.8125 (p90) cc_final: 0.7630 (p90) REVERT: A 292 PHE cc_start: 0.7860 (t80) cc_final: 0.7130 (t80) REVERT: A 338 ASP cc_start: 0.7416 (m-30) cc_final: 0.7149 (m-30) REVERT: A 386 SER cc_start: 0.8593 (t) cc_final: 0.8285 (t) REVERT: A 406 SER cc_start: 0.8621 (m) cc_final: 0.8376 (p) REVERT: B 74 MET cc_start: 0.0007 (mmp) cc_final: -0.0209 (mmp) REVERT: B 85 MET cc_start: 0.7960 (mmp) cc_final: 0.7448 (mmp) REVERT: B 108 LEU cc_start: 0.8672 (tt) cc_final: 0.8426 (tp) REVERT: B 115 ASN cc_start: 0.8200 (t0) cc_final: 0.7972 (t0) REVERT: B 122 LYS cc_start: 0.8311 (tmtt) cc_final: 0.7827 (tmtt) REVERT: B 127 MET cc_start: 0.7752 (mmp) cc_final: 0.7496 (mmp) REVERT: B 171 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 257 GLU cc_start: 0.7934 (mp0) cc_final: 0.7708 (mp0) REVERT: B 260 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 346 ASP cc_start: 0.7328 (p0) cc_final: 0.7103 (p0) REVERT: B 365 MET cc_start: 0.5093 (ppp) cc_final: 0.4528 (ppp) REVERT: C 58 ILE cc_start: 0.8462 (mt) cc_final: 0.8155 (tt) REVERT: C 79 TRP cc_start: 0.8945 (m100) cc_final: 0.8599 (m100) REVERT: C 82 LYS cc_start: 0.7970 (tptt) cc_final: 0.7672 (tptt) REVERT: C 102 VAL cc_start: 0.8458 (p) cc_final: 0.7977 (t) REVERT: C 110 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8237 (pttm) REVERT: C 195 MET cc_start: 0.8483 (mmm) cc_final: 0.8007 (mmm) REVERT: C 326 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8319 (mmmt) REVERT: D 74 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 106 LYS cc_start: 0.8597 (mppt) cc_final: 0.8164 (mppt) REVERT: D 110 VAL cc_start: 0.7975 (t) cc_final: 0.7663 (p) REVERT: D 115 MET cc_start: 0.7921 (mtm) cc_final: 0.7304 (mtm) REVERT: D 119 ASN cc_start: 0.8680 (m110) cc_final: 0.8174 (m110) REVERT: D 153 TYR cc_start: 0.8676 (m-80) cc_final: 0.8375 (m-80) REVERT: D 166 SER cc_start: 0.8347 (m) cc_final: 0.8133 (t) REVERT: D 186 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7721 (ttmm) REVERT: D 204 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7202 (mm-30) REVERT: E 14 LYS cc_start: 0.7819 (mptt) cc_final: 0.7537 (mptt) REVERT: E 19 MET cc_start: 0.7263 (mmm) cc_final: 0.6890 (tpt) REVERT: E 80 LYS cc_start: 0.7851 (mttp) cc_final: 0.7510 (mttp) REVERT: E 88 LYS cc_start: 0.8400 (tmmt) cc_final: 0.8012 (tmmt) REVERT: E 129 MET cc_start: 0.7793 (ttm) cc_final: 0.7586 (ttm) REVERT: F 39 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7595 (mm-30) REVERT: F 70 VAL cc_start: 0.8698 (p) cc_final: 0.8444 (t) REVERT: F 163 GLU cc_start: 0.7688 (tp30) cc_final: 0.6984 (tp30) REVERT: F 167 ASN cc_start: 0.7747 (m110) cc_final: 0.7450 (m-40) outliers start: 33 outliers final: 24 residues processed: 492 average time/residue: 0.1653 time to fit residues: 111.1918 Evaluate side-chains 498 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 473 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 179 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118718 restraints weight = 21641.841| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.11 r_work: 0.3324 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15373 Z= 0.148 Angle : 0.518 10.301 20807 Z= 0.271 Chirality : 0.044 0.259 2281 Planarity : 0.004 0.053 2674 Dihedral : 4.609 53.757 2053 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.97 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1863 helix: 1.62 (0.20), residues: 692 sheet: -0.23 (0.27), residues: 360 loop : 0.12 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 281 TYR 0.038 0.001 TYR E 74 PHE 0.022 0.002 PHE A 276 TRP 0.012 0.001 TRP C 131 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15373) covalent geometry : angle 0.51781 / 0.27 (20807) hydrogen bonds : bond 0.03473 / 2.28 ( 728) hydrogen bonds : angle 4.53304 / 3.19 ( 2019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 480 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: A 114 GLU cc_start: 0.8177 (pt0) cc_final: 0.7953 (pt0) REVERT: A 128 GLU cc_start: 0.8248 (tt0) cc_final: 0.7854 (tt0) REVERT: A 161 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7904 (mtm180) REVERT: A 229 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 230 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: A 255 GLN cc_start: 0.8689 (mp10) cc_final: 0.8360 (mm-40) REVERT: A 267 PHE cc_start: 0.8143 (p90) cc_final: 0.7609 (p90) REVERT: A 292 PHE cc_start: 0.7883 (t80) cc_final: 0.7126 (t80) REVERT: A 338 ASP cc_start: 0.7436 (m-30) cc_final: 0.7166 (m-30) REVERT: A 386 SER cc_start: 0.8580 (t) cc_final: 0.8257 (t) REVERT: A 406 SER cc_start: 0.8626 (m) cc_final: 0.8403 (p) REVERT: B 85 MET cc_start: 0.7937 (mmp) cc_final: 0.7413 (mmp) REVERT: B 108 LEU cc_start: 0.8660 (tt) cc_final: 0.8416 (tp) REVERT: B 122 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7825 (tmtt) REVERT: B 127 MET cc_start: 0.7750 (mmp) cc_final: 0.7495 (mmp) REVERT: B 171 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 214 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7989 (ttp80) REVERT: B 242 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 257 GLU cc_start: 0.7934 (mp0) cc_final: 0.7701 (mp0) REVERT: B 260 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 346 ASP cc_start: 0.7356 (p0) cc_final: 0.7133 (p0) REVERT: B 365 MET cc_start: 0.5167 (ppp) cc_final: 0.4583 (ppp) REVERT: C 58 ILE cc_start: 0.8430 (mt) cc_final: 0.8147 (tt) REVERT: C 79 TRP cc_start: 0.8948 (m100) cc_final: 0.8623 (m100) REVERT: C 82 LYS cc_start: 0.7965 (tptt) cc_final: 0.7627 (tptt) REVERT: C 90 LEU cc_start: 0.8576 (tp) cc_final: 0.8356 (tp) REVERT: C 102 VAL cc_start: 0.8439 (p) cc_final: 0.7990 (t) REVERT: C 110 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8269 (pttm) REVERT: C 119 VAL cc_start: 0.8719 (m) cc_final: 0.8327 (p) REVERT: C 195 MET cc_start: 0.8477 (mmm) cc_final: 0.8010 (mmm) REVERT: C 326 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8312 (mmtm) REVERT: D 74 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7451 (tm-30) REVERT: D 106 LYS cc_start: 0.8601 (mppt) cc_final: 0.8162 (mppt) REVERT: D 110 VAL cc_start: 0.7954 (t) cc_final: 0.7641 (p) REVERT: D 115 MET cc_start: 0.7929 (mtm) cc_final: 0.7325 (mtm) REVERT: D 119 ASN cc_start: 0.8713 (m110) cc_final: 0.8268 (m-40) REVERT: D 153 TYR cc_start: 0.8701 (m-80) cc_final: 0.8385 (m-80) REVERT: D 166 SER cc_start: 0.8366 (m) cc_final: 0.8121 (t) REVERT: D 186 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7702 (ttmm) REVERT: D 204 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7191 (mm-30) REVERT: E 14 LYS cc_start: 0.7804 (mptt) cc_final: 0.7528 (mptt) REVERT: E 80 LYS cc_start: 0.7836 (mttp) cc_final: 0.7503 (mttp) REVERT: E 88 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8025 (tmmt) REVERT: F 39 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7563 (mm-30) REVERT: F 70 VAL cc_start: 0.8691 (p) cc_final: 0.8427 (t) REVERT: F 139 MET cc_start: 0.8550 (mtt) cc_final: 0.8223 (mtp) REVERT: F 163 GLU cc_start: 0.7686 (tp30) cc_final: 0.6984 (tp30) REVERT: F 167 ASN cc_start: 0.7749 (m110) cc_final: 0.7432 (m-40) outliers start: 32 outliers final: 26 residues processed: 491 average time/residue: 0.1643 time to fit residues: 110.1844 Evaluate side-chains 499 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 472 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.0570 chunk 164 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN C 28 ASN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119203 restraints weight = 21546.766| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.10 r_work: 0.3339 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15373 Z= 0.129 Angle : 0.517 10.356 20807 Z= 0.270 Chirality : 0.044 0.216 2281 Planarity : 0.004 0.052 2674 Dihedral : 4.566 52.547 2053 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.27 % Allowed : 16.35 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1863 helix: 1.67 (0.20), residues: 692 sheet: -0.20 (0.27), residues: 360 loop : 0.15 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 281 TYR 0.042 0.001 TYR E 74 PHE 0.021 0.001 PHE A 276 TRP 0.012 0.001 TRP C 131 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15373) covalent geometry : angle 0.51662 / 0.27 (20807) hydrogen bonds : bond 0.03377 / 2.22 ( 728) hydrogen bonds : angle 4.48691 / 3.16 ( 2019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 477 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8666 (m-80) cc_final: 0.8456 (m-80) REVERT: A 79 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7191 (mtm-85) REVERT: A 128 GLU cc_start: 0.8258 (tt0) cc_final: 0.7704 (tt0) REVERT: A 229 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 230 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7785 (mtp-110) REVERT: A 255 GLN cc_start: 0.8689 (mp10) cc_final: 0.8360 (mm-40) REVERT: A 267 PHE cc_start: 0.8137 (p90) cc_final: 0.7552 (p90) REVERT: A 292 PHE cc_start: 0.7869 (t80) cc_final: 0.7113 (t80) REVERT: A 338 ASP cc_start: 0.7431 (m-30) cc_final: 0.7167 (m-30) REVERT: A 386 SER cc_start: 0.8591 (t) cc_final: 0.8251 (t) REVERT: A 406 SER cc_start: 0.8656 (m) cc_final: 0.8395 (p) REVERT: B 85 MET cc_start: 0.7939 (mmp) cc_final: 0.7637 (mmp) REVERT: B 108 LEU cc_start: 0.8670 (tt) cc_final: 0.8435 (tp) REVERT: B 122 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7802 (tmtt) REVERT: B 127 MET cc_start: 0.7693 (mmp) cc_final: 0.7453 (mmp) REVERT: B 171 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 214 ARG cc_start: 0.8247 (ttp80) cc_final: 0.8016 (ttp80) REVERT: B 242 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 257 GLU cc_start: 0.7924 (mp0) cc_final: 0.7699 (mp0) REVERT: B 260 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 365 MET cc_start: 0.5153 (ppp) cc_final: 0.4570 (ppp) REVERT: C 58 ILE cc_start: 0.8375 (mt) cc_final: 0.8103 (tt) REVERT: C 67 ILE cc_start: 0.8495 (mt) cc_final: 0.8114 (tt) REVERT: C 79 TRP cc_start: 0.8941 (m100) cc_final: 0.8588 (m100) REVERT: C 82 LYS cc_start: 0.7968 (tptt) cc_final: 0.7652 (tptt) REVERT: C 90 LEU cc_start: 0.8550 (tp) cc_final: 0.8330 (tp) REVERT: C 102 VAL cc_start: 0.8426 (p) cc_final: 0.7992 (t) REVERT: C 195 MET cc_start: 0.8465 (mmm) cc_final: 0.8019 (mmm) REVERT: D 74 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 106 LYS cc_start: 0.8600 (mppt) cc_final: 0.8143 (mppt) REVERT: D 110 VAL cc_start: 0.7918 (t) cc_final: 0.7578 (p) REVERT: D 153 TYR cc_start: 0.8634 (m-80) cc_final: 0.8317 (m-80) REVERT: D 166 SER cc_start: 0.8351 (m) cc_final: 0.8139 (t) REVERT: D 186 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7709 (ttmm) REVERT: D 204 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 14 LYS cc_start: 0.7775 (mptt) cc_final: 0.7490 (mptt) REVERT: E 80 LYS cc_start: 0.7810 (mttp) cc_final: 0.7459 (mttp) REVERT: E 88 LYS cc_start: 0.8368 (tmmt) cc_final: 0.7999 (tmmt) REVERT: E 129 MET cc_start: 0.7817 (ttm) cc_final: 0.7431 (ttm) REVERT: F 39 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 70 VAL cc_start: 0.8695 (p) cc_final: 0.8431 (t) REVERT: F 139 MET cc_start: 0.8567 (mtt) cc_final: 0.8240 (mtp) REVERT: F 163 GLU cc_start: 0.7670 (tp30) cc_final: 0.6980 (tp30) REVERT: F 167 ASN cc_start: 0.7726 (m110) cc_final: 0.7388 (m-40) outliers start: 37 outliers final: 27 residues processed: 489 average time/residue: 0.1664 time to fit residues: 110.8059 Evaluate side-chains 496 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 468 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 175 optimal weight: 0.0470 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 overall best weight: 1.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117481 restraints weight = 21856.459| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.11 r_work: 0.3306 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15373 Z= 0.205 Angle : 0.568 10.832 20807 Z= 0.296 Chirality : 0.046 0.204 2281 Planarity : 0.005 0.057 2674 Dihedral : 4.664 51.722 2052 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 17.03 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1863 helix: 1.54 (0.20), residues: 692 sheet: -0.25 (0.27), residues: 359 loop : 0.07 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 281 TYR 0.047 0.002 TYR E 74 PHE 0.021 0.002 PHE A 276 TRP 0.015 0.002 TRP H 224 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (15373) covalent geometry : angle 0.56808 / 0.30 (20807) hydrogen bonds : bond 0.03717 / 2.43 ( 728) hydrogen bonds : angle 4.59818 / 3.24 ( 2019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 478 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7220 (mtm-85) REVERT: A 128 GLU cc_start: 0.8263 (tt0) cc_final: 0.7726 (tt0) REVERT: A 230 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7802 (mtp-110) REVERT: A 240 LYS cc_start: 0.8489 (mttp) cc_final: 0.8287 (mttp) REVERT: A 255 GLN cc_start: 0.8706 (mp10) cc_final: 0.8358 (mm-40) REVERT: A 266 GLU cc_start: 0.7662 (pp20) cc_final: 0.7363 (pp20) REVERT: A 267 PHE cc_start: 0.8197 (p90) cc_final: 0.7325 (p90) REVERT: A 292 PHE cc_start: 0.7900 (t80) cc_final: 0.7167 (t80) REVERT: A 333 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.7696 (ttp80) REVERT: A 338 ASP cc_start: 0.7450 (m-30) cc_final: 0.7177 (m-30) REVERT: A 386 SER cc_start: 0.8622 (t) cc_final: 0.8266 (t) REVERT: A 406 SER cc_start: 0.8672 (m) cc_final: 0.8418 (p) REVERT: B 85 MET cc_start: 0.7989 (mmp) cc_final: 0.7662 (mmp) REVERT: B 108 LEU cc_start: 0.8701 (tt) cc_final: 0.8439 (tp) REVERT: B 122 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7859 (tmtt) REVERT: B 127 MET cc_start: 0.7707 (mmp) cc_final: 0.7412 (mmp) REVERT: B 171 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 192 TYR cc_start: 0.8820 (t80) cc_final: 0.8480 (t80) REVERT: B 242 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 257 GLU cc_start: 0.7958 (mp0) cc_final: 0.7729 (mp0) REVERT: B 260 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: B 339 LYS cc_start: 0.8643 (mptt) cc_final: 0.8300 (mptt) REVERT: B 365 MET cc_start: 0.5225 (ppp) cc_final: 0.4594 (ppp) REVERT: C 58 ILE cc_start: 0.8402 (mt) cc_final: 0.8130 (tt) REVERT: C 79 TRP cc_start: 0.8955 (m100) cc_final: 0.8649 (m100) REVERT: C 82 LYS cc_start: 0.7985 (tptt) cc_final: 0.7667 (tptt) REVERT: C 90 LEU cc_start: 0.8593 (tp) cc_final: 0.8353 (tp) REVERT: C 195 MET cc_start: 0.8466 (mmm) cc_final: 0.8015 (mmm) REVERT: C 326 LYS cc_start: 0.8540 (mmmm) cc_final: 0.8323 (mmmm) REVERT: D 74 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 106 LYS cc_start: 0.8633 (mppt) cc_final: 0.8165 (mppt) REVERT: D 110 VAL cc_start: 0.7995 (t) cc_final: 0.7682 (p) REVERT: D 153 TYR cc_start: 0.8688 (m-80) cc_final: 0.8440 (m-80) REVERT: D 166 SER cc_start: 0.8402 (m) cc_final: 0.8200 (t) REVERT: D 186 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7746 (ttmm) REVERT: D 204 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7269 (mm-30) REVERT: E 14 LYS cc_start: 0.7801 (mptt) cc_final: 0.7526 (mptt) REVERT: E 80 LYS cc_start: 0.7850 (mttp) cc_final: 0.7621 (mttp) REVERT: E 88 LYS cc_start: 0.8403 (tmmt) cc_final: 0.8035 (tmmt) REVERT: E 129 MET cc_start: 0.7877 (ttm) cc_final: 0.7486 (ttm) REVERT: F 70 VAL cc_start: 0.8671 (p) cc_final: 0.8429 (t) REVERT: F 139 MET cc_start: 0.8628 (mtt) cc_final: 0.8308 (mtp) REVERT: F 163 GLU cc_start: 0.7713 (tp30) cc_final: 0.6985 (tp30) REVERT: F 167 ASN cc_start: 0.7822 (m110) cc_final: 0.7484 (m-40) REVERT: H 200 MET cc_start: 0.7637 (mmm) cc_final: 0.7367 (mmm) outliers start: 35 outliers final: 29 residues processed: 489 average time/residue: 0.1636 time to fit residues: 109.4869 Evaluate side-chains 501 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 471 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 0.0070 chunk 155 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 49 optimal weight: 0.0170 chunk 91 optimal weight: 2.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119664 restraints weight = 21623.621| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.12 r_work: 0.3333 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15373 Z= 0.122 Angle : 0.541 10.363 20807 Z= 0.284 Chirality : 0.044 0.192 2281 Planarity : 0.004 0.055 2674 Dihedral : 4.550 50.028 2052 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.91 % Allowed : 18.07 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1863 helix: 1.59 (0.20), residues: 693 sheet: -0.19 (0.28), residues: 358 loop : 0.12 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 281 TYR 0.048 0.002 TYR E 74 PHE 0.020 0.001 PHE A 276 TRP 0.011 0.001 TRP C 131 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15373) covalent geometry : angle 0.54136 / 0.28 (20807) hydrogen bonds : bond 0.03368 / 2.21 ( 728) hydrogen bonds : angle 4.51787 / 3.19 ( 2019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 465 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8662 (m-80) cc_final: 0.8362 (m-10) REVERT: A 79 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: A 94 GLU cc_start: 0.8170 (tt0) cc_final: 0.7969 (tt0) REVERT: A 128 GLU cc_start: 0.8263 (tt0) cc_final: 0.7885 (tt0) REVERT: A 229 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 230 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7818 (mtp-110) REVERT: A 255 GLN cc_start: 0.8673 (mp10) cc_final: 0.8330 (mm-40) REVERT: A 267 PHE cc_start: 0.8206 (p90) cc_final: 0.7555 (p90) REVERT: A 292 PHE cc_start: 0.7904 (t80) cc_final: 0.7147 (t80) REVERT: A 333 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7602 (ttp80) REVERT: A 338 ASP cc_start: 0.7422 (m-30) cc_final: 0.7147 (m-30) REVERT: A 386 SER cc_start: 0.8586 (t) cc_final: 0.8230 (t) REVERT: A 406 SER cc_start: 0.8588 (m) cc_final: 0.8310 (p) REVERT: B 85 MET cc_start: 0.8000 (mmp) cc_final: 0.7669 (mmp) REVERT: B 108 LEU cc_start: 0.8685 (tt) cc_final: 0.8441 (tp) REVERT: B 122 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7838 (tmtt) REVERT: B 127 MET cc_start: 0.7735 (mmp) cc_final: 0.7425 (mmp) REVERT: B 171 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 184 ILE cc_start: 0.8413 (mt) cc_final: 0.8087 (tt) REVERT: B 242 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 257 GLU cc_start: 0.7954 (mp0) cc_final: 0.7707 (mp0) REVERT: B 260 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 339 LYS cc_start: 0.8527 (mptt) cc_final: 0.8206 (mptt) REVERT: B 365 MET cc_start: 0.5151 (ppp) cc_final: 0.4532 (ppp) REVERT: C 58 ILE cc_start: 0.8348 (mt) cc_final: 0.8062 (tt) REVERT: C 67 ILE cc_start: 0.8491 (mt) cc_final: 0.8123 (tt) REVERT: C 79 TRP cc_start: 0.8934 (m100) cc_final: 0.8631 (m100) REVERT: C 82 LYS cc_start: 0.7991 (tptt) cc_final: 0.7680 (tptt) REVERT: C 90 LEU cc_start: 0.8551 (tp) cc_final: 0.8324 (tp) REVERT: C 195 MET cc_start: 0.8410 (mmm) cc_final: 0.7981 (mmm) REVERT: C 326 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8235 (mmmm) REVERT: D 74 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7523 (tm-30) REVERT: D 106 LYS cc_start: 0.8612 (mppt) cc_final: 0.8152 (mppt) REVERT: D 110 VAL cc_start: 0.7961 (t) cc_final: 0.7664 (p) REVERT: D 141 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.8088 (ptp90) REVERT: D 153 TYR cc_start: 0.8631 (m-80) cc_final: 0.8293 (m-80) REVERT: D 186 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7714 (ttmm) REVERT: D 204 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7202 (mm-30) REVERT: E 14 LYS cc_start: 0.7788 (mptt) cc_final: 0.7503 (mptt) REVERT: E 88 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7997 (tmmt) REVERT: E 129 MET cc_start: 0.7870 (ttm) cc_final: 0.7489 (ttm) REVERT: F 70 VAL cc_start: 0.8712 (p) cc_final: 0.8470 (t) REVERT: F 139 MET cc_start: 0.8580 (mtt) cc_final: 0.8212 (mtp) REVERT: F 163 GLU cc_start: 0.7685 (tp30) cc_final: 0.6970 (tp30) REVERT: F 167 ASN cc_start: 0.7737 (m110) cc_final: 0.7401 (m-40) REVERT: H 200 MET cc_start: 0.7629 (mmm) cc_final: 0.7336 (mmm) outliers start: 31 outliers final: 25 residues processed: 476 average time/residue: 0.1697 time to fit residues: 109.7866 Evaluate side-chains 483 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 457 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 118 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118488 restraints weight = 21748.400| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.12 r_work: 0.3323 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15373 Z= 0.169 Angle : 0.564 10.667 20807 Z= 0.296 Chirality : 0.045 0.189 2281 Planarity : 0.005 0.056 2674 Dihedral : 4.600 49.131 2052 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.97 % Allowed : 18.01 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1863 helix: 1.58 (0.20), residues: 693 sheet: -0.27 (0.27), residues: 358 loop : 0.03 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 281 TYR 0.053 0.002 TYR E 74 PHE 0.021 0.002 PHE A 276 TRP 0.014 0.001 TRP C 219 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (15373) covalent geometry : angle 0.56361 / 0.30 (20807) hydrogen bonds : bond 0.03575 / 2.36 ( 728) hydrogen bonds : angle 4.56385 / 3.22 ( 2019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 472 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: A 128 GLU cc_start: 0.8283 (tt0) cc_final: 0.7897 (tt0) REVERT: A 229 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 230 ARG cc_start: 0.8229 (mtp-110) cc_final: 0.7821 (mtp-110) REVERT: A 255 GLN cc_start: 0.8686 (mp10) cc_final: 0.8347 (mm-40) REVERT: A 266 GLU cc_start: 0.7651 (pp20) cc_final: 0.7328 (pp20) REVERT: A 292 PHE cc_start: 0.7881 (t80) cc_final: 0.7135 (t80) REVERT: A 333 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7648 (ttp80) REVERT: A 338 ASP cc_start: 0.7448 (m-30) cc_final: 0.7182 (m-30) REVERT: A 386 SER cc_start: 0.8615 (t) cc_final: 0.8246 (t) REVERT: A 406 SER cc_start: 0.8580 (m) cc_final: 0.8338 (p) REVERT: B 108 LEU cc_start: 0.8680 (tt) cc_final: 0.8447 (tp) REVERT: B 122 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7855 (tmtt) REVERT: B 127 MET cc_start: 0.7775 (mmp) cc_final: 0.7470 (mmp) REVERT: B 171 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 184 ILE cc_start: 0.8422 (mt) cc_final: 0.8111 (tt) REVERT: B 214 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7982 (ttp80) REVERT: B 242 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 257 GLU cc_start: 0.7980 (mp0) cc_final: 0.7730 (mp0) REVERT: B 260 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 339 LYS cc_start: 0.8554 (mptt) cc_final: 0.8227 (mptt) REVERT: B 365 MET cc_start: 0.5153 (ppp) cc_final: 0.4519 (ppp) REVERT: C 58 ILE cc_start: 0.8351 (mt) cc_final: 0.8120 (tt) REVERT: C 79 TRP cc_start: 0.8942 (m100) cc_final: 0.8642 (m100) REVERT: C 82 LYS cc_start: 0.7945 (tptt) cc_final: 0.7650 (tptt) REVERT: C 90 LEU cc_start: 0.8575 (tp) cc_final: 0.8330 (tp) REVERT: C 102 VAL cc_start: 0.8325 (p) cc_final: 0.8029 (t) REVERT: C 178 GLU cc_start: 0.7996 (pm20) cc_final: 0.7565 (pm20) REVERT: C 195 MET cc_start: 0.8441 (mmm) cc_final: 0.7957 (mmm) REVERT: C 326 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8313 (mmmm) REVERT: D 37 ASP cc_start: 0.8179 (t0) cc_final: 0.7951 (t70) REVERT: D 74 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 106 LYS cc_start: 0.8621 (mppt) cc_final: 0.8144 (mppt) REVERT: D 110 VAL cc_start: 0.7969 (t) cc_final: 0.7670 (p) REVERT: D 141 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.8092 (ptp90) REVERT: D 153 TYR cc_start: 0.8627 (m-80) cc_final: 0.8285 (m-80) REVERT: D 166 SER cc_start: 0.8229 (t) cc_final: 0.7994 (m) REVERT: D 186 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7743 (ttmm) REVERT: D 204 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7229 (mm-30) REVERT: E 14 LYS cc_start: 0.7819 (mptt) cc_final: 0.7512 (mptt) REVERT: E 80 LYS cc_start: 0.7800 (mttp) cc_final: 0.7528 (mtmp) REVERT: E 88 LYS cc_start: 0.8381 (tmmt) cc_final: 0.8024 (tmmt) REVERT: E 129 MET cc_start: 0.7871 (ttm) cc_final: 0.7497 (ttm) REVERT: F 70 VAL cc_start: 0.8684 (p) cc_final: 0.8445 (t) REVERT: F 139 MET cc_start: 0.8606 (mtt) cc_final: 0.8272 (mtp) REVERT: F 163 GLU cc_start: 0.7725 (tp30) cc_final: 0.6991 (tp30) REVERT: F 167 ASN cc_start: 0.7779 (m110) cc_final: 0.7434 (m-40) REVERT: H 200 MET cc_start: 0.7659 (mmm) cc_final: 0.7360 (mmm) outliers start: 32 outliers final: 29 residues processed: 484 average time/residue: 0.1578 time to fit residues: 104.6144 Evaluate side-chains 500 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 470 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 172 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 177 optimal weight: 0.0980 chunk 41 optimal weight: 0.0060 chunk 19 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 91 optimal weight: 0.0050 chunk 134 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 373 GLN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 245 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121321 restraints weight = 21649.263| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.13 r_work: 0.3373 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15373 Z= 0.106 Angle : 0.543 10.346 20807 Z= 0.285 Chirality : 0.044 0.184 2281 Planarity : 0.004 0.053 2674 Dihedral : 4.465 47.013 2052 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.78 % Allowed : 18.56 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1863 helix: 1.64 (0.20), residues: 695 sheet: -0.18 (0.27), residues: 360 loop : 0.14 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 281 TYR 0.049 0.002 TYR E 74 PHE 0.020 0.001 PHE A 276 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15373) covalent geometry : angle 0.54311 / 0.28 (20807) hydrogen bonds : bond 0.03225 / 2.13 ( 728) hydrogen bonds : angle 4.46243 / 3.15 ( 2019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4479.98 seconds wall clock time: 77 minutes 35.34 seconds (4655.34 seconds total)