Starting phenix.real_space_refine on Fri Jun 13 13:48:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpn_22416/06_2025/7jpn_22416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpn_22416/06_2025/7jpn_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_22416/06_2025/7jpn_22416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpn_22416/06_2025/7jpn_22416.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpn_22416/06_2025/7jpn_22416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpn_22416/06_2025/7jpn_22416.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.58, per 1000 atoms: 0.64 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.01 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: 5.17 Time building geometry restraints manager: 4.20 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: 8281 17.70 - 35.41: 786 35.41 - 53.11: 179 53.11 - 70.81: 30 70.81 - 88.52: 12 Dihedral angle restraints: 9288 sinusoidal: 3814 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 9285 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 36.780 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 14.752 88.518 5756 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.037 0.002 TRP H 224 HIS 0.005 0.001 HIS D 254 PHE 0.029 0.002 PHE A 283 TYR 0.029 0.002 TYR A 125 ARG 0.009 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.12316 ( 728) hydrogen bonds : angle 5.74829 ( 2019) covalent geometry : bond 0.00377 (15373) covalent geometry : angle 0.63179 (20807) *********************** 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 : 1.599 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: 0.6114 (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: 0.8268 (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: 0.7052 (pm20) cc_final: 0.6778 (pm20) REVERT: C 225 THR cc_start: 0.8241 (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: 0.3650 time to fit residues: 244.2058 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 : 1.715 ------------------------------------------------------------------------------- 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 155 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119394 restraints weight = 21738.758| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.11 r_work: 0.3337 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15373 Z= 0.134 Angle : 0.530 8.277 20807 Z= 0.281 Chirality : 0.044 0.211 2281 Planarity : 0.004 0.053 2674 Dihedral : 6.666 85.151 2117 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.04 % Allowed : 8.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1863 helix: 1.55 (0.20), residues: 688 sheet: -0.17 (0.27), residues: 354 loop : 0.03 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 160 HIS 0.004 0.001 HIS C 33 PHE 0.022 0.002 PHE B 340 TYR 0.022 0.002 TYR E 74 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 728) hydrogen bonds : angle 4.78609 ( 2019) covalent geometry : bond 0.00303 (15373) covalent geometry : angle 0.53017 (20807) *********************** 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 501 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 484 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.8580 (mm) cc_final: 0.8242 (mm) REVERT: A 72 TYR cc_start: 0.8615 (m-80) cc_final: 0.8370 (m-80) REVERT: A 79 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7304 (mtm-85) REVERT: A 85 ASP cc_start: 0.7298 (t0) cc_final: 0.7066 (t0) REVERT: A 123 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7816 (mtt-85) REVERT: A 128 GLU cc_start: 0.8314 (tt0) cc_final: 0.7946 (tt0) REVERT: A 188 SER cc_start: 0.8608 (p) cc_final: 0.8404 (m) REVERT: A 221 LEU cc_start: 0.8445 (tp) cc_final: 0.8219 (tp) REVERT: A 229 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 255 GLN cc_start: 0.8720 (mp10) cc_final: 0.8450 (mm-40) REVERT: A 292 PHE cc_start: 0.7763 (t80) cc_final: 0.7083 (t80) REVERT: A 333 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8240 (ttm-80) REVERT: A 338 ASP cc_start: 0.7369 (m-30) cc_final: 0.7086 (m-30) REVERT: A 344 ASP cc_start: 0.7896 (m-30) cc_final: 0.7613 (m-30) REVERT: A 389 GLU cc_start: 0.8006 (tt0) cc_final: 0.7634 (tm-30) REVERT: B 74 MET cc_start: 0.0372 (mmp) cc_final: -0.0165 (mmp) REVERT: B 85 MET cc_start: 0.7957 (mmp) cc_final: 0.7507 (mmp) REVERT: B 115 ASN cc_start: 0.8162 (t0) cc_final: 0.7902 (t0) REVERT: B 127 MET cc_start: 0.7711 (mmp) cc_final: 0.7433 (mmp) REVERT: B 145 THR cc_start: 0.8440 (m) cc_final: 0.8177 (m) REVERT: B 171 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 257 GLU cc_start: 0.7925 (mp0) cc_final: 0.7635 (mp0) REVERT: B 260 GLU cc_start: 0.7561 (mp0) cc_final: 0.6992 (mp0) REVERT: C 58 ILE cc_start: 0.8408 (mt) cc_final: 0.8027 (tt) REVERT: C 79 TRP cc_start: 0.8960 (m100) cc_final: 0.8440 (m100) REVERT: C 92 ILE cc_start: 0.8361 (pt) cc_final: 0.8137 (pt) REVERT: C 178 GLU cc_start: 0.7941 (pm20) cc_final: 0.7546 (pm20) REVERT: C 195 MET cc_start: 0.8421 (mmm) cc_final: 0.8024 (mmm) REVERT: C 326 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8217 (mmmt) REVERT: D 5 GLU cc_start: 0.7537 (pm20) cc_final: 0.7104 (pm20) REVERT: D 65 LYS cc_start: 0.8328 (mttp) cc_final: 0.8080 (mttp) REVERT: D 74 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 106 LYS cc_start: 0.8512 (mppt) cc_final: 0.8134 (mppt) REVERT: D 115 MET cc_start: 0.7510 (mtm) cc_final: 0.7034 (mtt) REVERT: D 119 ASN cc_start: 0.8639 (m110) cc_final: 0.8278 (m-40) REVERT: D 182 MET cc_start: 0.8042 (mmm) cc_final: 0.7781 (mmm) REVERT: D 186 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7790 (ttmm) REVERT: D 204 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D 219 ASN cc_start: 0.8132 (m-40) cc_final: 0.7811 (m-40) REVERT: D 230 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8082 (ptp90) REVERT: E 14 LYS cc_start: 0.7822 (mptt) cc_final: 0.7521 (mptt) REVERT: E 63 GLU cc_start: 0.8157 (mp0) cc_final: 0.7819 (mp0) REVERT: E 80 LYS cc_start: 0.7802 (mttp) cc_final: 0.7524 (mttp) REVERT: E 88 LYS cc_start: 0.8342 (tmmt) cc_final: 0.7968 (tmmt) REVERT: E 129 MET cc_start: 0.7715 (ttm) cc_final: 0.7508 (ttm) REVERT: F 39 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7529 (mm-30) REVERT: F 45 GLU cc_start: 0.8237 (pm20) cc_final: 0.7989 (pm20) REVERT: F 141 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7205 (mm-30) REVERT: F 163 GLU cc_start: 0.7676 (tp30) cc_final: 0.6972 (tp30) REVERT: F 167 ASN cc_start: 0.7651 (m110) cc_final: 0.7369 (m-40) REVERT: H 222 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7134 (mm-30) outliers start: 17 outliers final: 9 residues processed: 490 average time/residue: 0.3656 time to fit residues: 241.1109 Evaluate side-chains 482 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 473 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 LEU 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 20 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 287 GLN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 245 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 = 0.3765 r_free = 0.3765 target = 0.140211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116779 restraints weight = 21723.007| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.11 r_work: 0.3296 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15373 Z= 0.241 Angle : 0.558 9.672 20807 Z= 0.296 Chirality : 0.047 0.177 2281 Planarity : 0.004 0.056 2674 Dihedral : 6.449 86.568 2115 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.54 % Allowed : 11.62 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1863 helix: 1.49 (0.20), residues: 688 sheet: -0.20 (0.28), residues: 357 loop : -0.02 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 224 HIS 0.009 0.001 HIS D 245 PHE 0.022 0.002 PHE A 276 TYR 0.034 0.002 TYR B 298 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 728) hydrogen bonds : angle 4.74708 ( 2019) covalent geometry : bond 0.00558 (15373) covalent geometry : angle 0.55837 (20807) *********************** 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 517 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 492 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7300 (mtm-85) REVERT: A 94 GLU cc_start: 0.8146 (tt0) cc_final: 0.7938 (tt0) REVERT: A 123 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7921 (mtt-85) REVERT: A 128 GLU cc_start: 0.8272 (tt0) cc_final: 0.7753 (tt0) REVERT: A 188 SER cc_start: 0.8621 (p) cc_final: 0.8420 (m) REVERT: A 221 LEU cc_start: 0.8438 (tp) cc_final: 0.8233 (tp) REVERT: A 255 GLN cc_start: 0.8753 (mp10) cc_final: 0.8433 (mm-40) REVERT: A 292 PHE cc_start: 0.7851 (t80) cc_final: 0.7149 (t80) REVERT: A 338 ASP cc_start: 0.7422 (m-30) cc_final: 0.7144 (m-30) REVERT: A 386 SER cc_start: 0.8635 (t) cc_final: 0.8401 (t) REVERT: A 389 GLU cc_start: 0.8048 (tt0) cc_final: 0.7741 (tm-30) REVERT: A 406 SER cc_start: 0.8630 (m) cc_final: 0.8418 (p) REVERT: B 74 MET cc_start: 0.0325 (mmp) cc_final: -0.0142 (mmp) REVERT: B 85 MET cc_start: 0.8014 (mmp) cc_final: 0.7501 (mmp) REVERT: B 115 ASN cc_start: 0.8195 (t0) cc_final: 0.7950 (t0) REVERT: B 127 MET cc_start: 0.7706 (mmp) cc_final: 0.7436 (mmp) REVERT: B 171 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 257 GLU cc_start: 0.7916 (mp0) cc_final: 0.7660 (mp0) REVERT: B 260 GLU cc_start: 0.7787 (mp0) cc_final: 0.7125 (mp0) REVERT: B 340 PHE cc_start: 0.8178 (t80) cc_final: 0.7795 (t80) REVERT: B 346 ASP cc_start: 0.7405 (p0) cc_final: 0.7177 (p0) REVERT: B 365 MET cc_start: 0.5086 (ppp) cc_final: 0.4688 (ppp) REVERT: C 110 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8308 (mtmm) REVERT: C 195 MET cc_start: 0.8492 (mmm) cc_final: 0.8022 (mmm) REVERT: C 326 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8337 (mmmt) REVERT: D 5 GLU cc_start: 0.7543 (pm20) cc_final: 0.7067 (pm20) REVERT: D 74 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 106 LYS cc_start: 0.8565 (mppt) cc_final: 0.8160 (mppt) REVERT: D 115 MET cc_start: 0.7826 (mtm) cc_final: 0.7260 (mtm) REVERT: D 119 ASN cc_start: 0.8639 (m110) cc_final: 0.8199 (m-40) REVERT: D 166 SER cc_start: 0.8292 (m) cc_final: 0.8012 (t) REVERT: D 182 MET cc_start: 0.7969 (mmm) cc_final: 0.7689 (mmm) REVERT: D 186 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7785 (ttmm) REVERT: D 204 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7249 (mm-30) REVERT: E 14 LYS cc_start: 0.7804 (mptt) cc_final: 0.7534 (mptt) REVERT: E 88 LYS cc_start: 0.8350 (tmmt) cc_final: 0.7973 (tmmt) REVERT: E 129 MET cc_start: 0.7693 (ttm) cc_final: 0.7476 (ttm) REVERT: F 39 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7548 (mm-30) REVERT: F 141 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7218 (mm-30) REVERT: F 163 GLU cc_start: 0.7753 (tp30) cc_final: 0.7014 (tp30) REVERT: F 167 ASN cc_start: 0.7773 (m110) cc_final: 0.7488 (m-40) outliers start: 25 outliers final: 18 residues processed: 498 average time/residue: 0.3739 time to fit residues: 251.0435 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 : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL 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 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 75 optimal weight: 0.0670 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 145 HIS 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 = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118670 restraints weight = 21689.322| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.11 r_work: 0.3324 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15373 Z= 0.139 Angle : 0.520 9.914 20807 Z= 0.274 Chirality : 0.044 0.149 2281 Planarity : 0.004 0.053 2674 Dihedral : 6.213 85.465 2115 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.54 % Allowed : 13.95 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1863 helix: 1.54 (0.20), residues: 694 sheet: -0.15 (0.28), residues: 354 loop : 0.00 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 224 HIS 0.006 0.001 HIS D 245 PHE 0.021 0.002 PHE A 276 TYR 0.031 0.002 TYR B 325 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 728) hydrogen bonds : angle 4.66299 ( 2019) covalent geometry : bond 0.00323 (15373) covalent geometry : angle 0.51969 (20807) *********************** 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 507 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 482 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.8595 (mm) cc_final: 0.8281 (mm) REVERT: A 79 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: A 128 GLU cc_start: 0.8248 (tt0) cc_final: 0.7899 (tt0) REVERT: A 230 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7816 (mtp-110) REVERT: A 255 GLN cc_start: 0.8705 (mp10) cc_final: 0.8388 (mm-40) REVERT: A 267 PHE cc_start: 0.8022 (p90) cc_final: 0.7593 (p90) REVERT: A 292 PHE cc_start: 0.7835 (t80) cc_final: 0.7094 (t80) REVERT: A 338 ASP cc_start: 0.7410 (m-30) cc_final: 0.7129 (m-30) REVERT: A 386 SER cc_start: 0.8637 (t) cc_final: 0.8351 (t) REVERT: A 406 SER cc_start: 0.8616 (m) cc_final: 0.8397 (p) REVERT: B 74 MET cc_start: 0.0184 (mmp) cc_final: -0.0205 (mmp) REVERT: B 85 MET cc_start: 0.7956 (mmp) cc_final: 0.7437 (mmp) REVERT: B 108 LEU cc_start: 0.8668 (tt) cc_final: 0.8397 (tp) REVERT: B 115 ASN cc_start: 0.8163 (t0) cc_final: 0.7956 (t0) REVERT: B 122 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7802 (tmtt) REVERT: B 171 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 242 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 257 GLU cc_start: 0.7907 (mp0) cc_final: 0.7674 (mp0) REVERT: B 260 GLU cc_start: 0.7765 (mp0) cc_final: 0.7125 (mp0) REVERT: B 346 ASP cc_start: 0.7314 (p0) cc_final: 0.6963 (p0) REVERT: B 365 MET cc_start: 0.5063 (ppp) cc_final: 0.4587 (ppp) REVERT: C 58 ILE cc_start: 0.8469 (mt) cc_final: 0.8142 (tt) REVERT: C 79 TRP cc_start: 0.8954 (m100) cc_final: 0.8595 (m100) REVERT: C 102 VAL cc_start: 0.8456 (p) cc_final: 0.7989 (t) REVERT: C 153 ASN cc_start: 0.8457 (p0) cc_final: 0.8140 (p0) REVERT: C 195 MET cc_start: 0.8503 (mmm) cc_final: 0.8059 (mmm) REVERT: C 326 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8331 (mmmt) REVERT: D 74 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7473 (tm-30) REVERT: D 106 LYS cc_start: 0.8582 (mppt) cc_final: 0.8153 (mppt) REVERT: D 115 MET cc_start: 0.7838 (mtm) cc_final: 0.7282 (mtm) REVERT: D 119 ASN cc_start: 0.8713 (m110) cc_final: 0.8278 (m-40) REVERT: D 141 ARG cc_start: 0.8545 (ptp-110) cc_final: 0.8297 (ptp-110) REVERT: D 166 SER cc_start: 0.8312 (m) cc_final: 0.8019 (t) REVERT: D 182 MET cc_start: 0.7980 (mmm) cc_final: 0.7708 (mmm) REVERT: D 186 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7811 (ttmm) REVERT: D 204 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7189 (mm-30) REVERT: D 266 MET cc_start: 0.8214 (mtt) cc_final: 0.7886 (mtp) REVERT: E 14 LYS cc_start: 0.7812 (mptt) cc_final: 0.7531 (mptt) REVERT: E 80 LYS cc_start: 0.7863 (mttp) cc_final: 0.7528 (mttp) REVERT: E 88 LYS cc_start: 0.8332 (tmmt) cc_final: 0.7952 (tmmt) REVERT: F 39 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7540 (mm-30) REVERT: F 70 VAL cc_start: 0.8670 (p) cc_final: 0.8426 (t) REVERT: F 163 GLU cc_start: 0.7703 (tp30) cc_final: 0.6977 (tp30) REVERT: F 167 ASN cc_start: 0.7727 (m110) cc_final: 0.7425 (m-40) REVERT: H 222 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7274 (tm-30) outliers start: 25 outliers final: 18 residues processed: 488 average time/residue: 0.3799 time to fit residues: 249.1935 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 : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 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 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 E residue 56 LYS Chi-restraints excluded: chain E residue 73 LEU 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 53 optimal weight: 3.9990 chunk 178 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 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** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116616 restraints weight = 21869.541| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.10 r_work: 0.3290 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15373 Z= 0.253 Angle : 0.562 10.691 20807 Z= 0.297 Chirality : 0.047 0.174 2281 Planarity : 0.004 0.053 2674 Dihedral : 6.329 87.104 2115 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.27 % Allowed : 14.75 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1863 helix: 1.43 (0.20), residues: 692 sheet: -0.29 (0.28), residues: 358 loop : -0.03 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 224 HIS 0.007 0.001 HIS F 137 PHE 0.024 0.002 PHE A 276 TYR 0.032 0.002 TYR E 74 ARG 0.008 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 728) hydrogen bonds : angle 4.70449 ( 2019) covalent geometry : bond 0.00585 (15373) covalent geometry : angle 0.56194 (20807) *********************** 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 520 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 483 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7251 (mtm-85) REVERT: A 128 GLU cc_start: 0.8255 (tt0) cc_final: 0.7790 (tt0) REVERT: A 229 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 230 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7778 (mtp-110) REVERT: A 240 LYS cc_start: 0.8509 (mttp) cc_final: 0.8299 (mttp) REVERT: A 255 GLN cc_start: 0.8705 (mp10) cc_final: 0.8372 (mm-40) REVERT: A 267 PHE cc_start: 0.8087 (p90) cc_final: 0.7666 (p90) REVERT: A 292 PHE cc_start: 0.7881 (t80) cc_final: 0.7153 (t80) REVERT: A 338 ASP cc_start: 0.7462 (m-30) cc_final: 0.7195 (m-30) REVERT: A 386 SER cc_start: 0.8643 (t) cc_final: 0.8337 (t) REVERT: A 406 SER cc_start: 0.8643 (m) cc_final: 0.8434 (p) REVERT: B 74 MET cc_start: 0.0127 (mmp) cc_final: -0.0156 (mmp) REVERT: B 85 MET cc_start: 0.7978 (mmp) cc_final: 0.7470 (mmp) REVERT: B 115 ASN cc_start: 0.8225 (t0) cc_final: 0.8015 (t0) REVERT: B 122 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7881 (tmtt) REVERT: B 171 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 214 ARG cc_start: 0.8240 (ttp80) cc_final: 0.8022 (ttp80) REVERT: B 242 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 257 GLU cc_start: 0.7946 (mp0) cc_final: 0.7713 (mp0) REVERT: B 260 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: B 339 LYS cc_start: 0.8659 (mptt) cc_final: 0.8310 (mptt) REVERT: B 346 ASP cc_start: 0.7375 (p0) cc_final: 0.7123 (p0) REVERT: B 365 MET cc_start: 0.5018 (ppp) cc_final: 0.4459 (ppp) REVERT: C 58 ILE cc_start: 0.8512 (mt) cc_final: 0.8179 (tt) REVERT: C 82 LYS cc_start: 0.7958 (tptt) cc_final: 0.7642 (tptt) REVERT: D 74 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 106 LYS cc_start: 0.8613 (mppt) cc_final: 0.8167 (mppt) REVERT: D 110 VAL cc_start: 0.8018 (t) cc_final: 0.7716 (p) REVERT: D 115 MET cc_start: 0.8001 (mtm) cc_final: 0.7718 (mtm) REVERT: D 147 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8137 (mtp-110) REVERT: D 166 SER cc_start: 0.8395 (m) cc_final: 0.8103 (t) REVERT: D 182 MET cc_start: 0.7941 (mmm) cc_final: 0.7654 (mmm) REVERT: D 186 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7811 (ttmm) REVERT: D 204 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7313 (mm-30) REVERT: D 266 MET cc_start: 0.8222 (mtt) cc_final: 0.7951 (mtp) REVERT: E 14 LYS cc_start: 0.7775 (mptt) cc_final: 0.7506 (mptt) REVERT: E 69 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8346 (mp) REVERT: E 80 LYS cc_start: 0.7964 (mttp) cc_final: 0.7689 (mttp) REVERT: E 88 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7983 (tmmt) REVERT: F 39 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7571 (mm-30) REVERT: F 70 VAL cc_start: 0.8635 (p) cc_final: 0.8419 (t) REVERT: F 163 GLU cc_start: 0.7741 (tp30) cc_final: 0.6991 (tp30) REVERT: F 167 ASN cc_start: 0.7850 (m110) cc_final: 0.7539 (m-40) outliers start: 37 outliers final: 29 residues processed: 497 average time/residue: 0.3515 time to fit residues: 235.4504 Evaluate side-chains 502 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 471 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 143 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 227 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 293 THR 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 170 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 13 GLU 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 E residue 69 ILE Chi-restraints excluded: chain E residue 73 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 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 172 optimal weight: 0.3980 chunk 114 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 119 ASN D 245 HIS F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119159 restraints weight = 21831.998| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.12 r_work: 0.3338 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15373 Z= 0.113 Angle : 0.508 10.386 20807 Z= 0.268 Chirality : 0.043 0.144 2281 Planarity : 0.004 0.055 2674 Dihedral : 6.054 89.796 2115 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 16.04 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1863 helix: 1.57 (0.20), residues: 693 sheet: -0.24 (0.28), residues: 357 loop : 0.02 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.003 0.001 HIS C 206 PHE 0.020 0.001 PHE A 276 TYR 0.037 0.001 TYR E 74 ARG 0.008 0.001 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 728) hydrogen bonds : angle 4.54145 ( 2019) covalent geometry : bond 0.00258 (15373) covalent geometry : angle 0.50848 (20807) *********************** 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 515 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 481 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.8550 (mm) cc_final: 0.8233 (mm) REVERT: A 79 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: A 128 GLU cc_start: 0.8260 (tt0) cc_final: 0.7974 (tt0) REVERT: A 229 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 230 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7793 (mtp-110) REVERT: A 255 GLN cc_start: 0.8692 (mp10) cc_final: 0.8364 (mm-40) REVERT: A 267 PHE cc_start: 0.8055 (p90) cc_final: 0.7593 (p90) REVERT: A 292 PHE cc_start: 0.7888 (t80) cc_final: 0.7146 (t80) REVERT: A 338 ASP cc_start: 0.7391 (m-30) cc_final: 0.7107 (m-30) REVERT: A 386 SER cc_start: 0.8607 (t) cc_final: 0.8281 (t) REVERT: A 406 SER cc_start: 0.8610 (m) cc_final: 0.8370 (p) REVERT: B 74 MET cc_start: 0.0021 (mmp) cc_final: -0.0191 (mmp) REVERT: B 85 MET cc_start: 0.7980 (mmp) cc_final: 0.7440 (mmp) REVERT: B 108 LEU cc_start: 0.8640 (tt) cc_final: 0.8399 (tp) REVERT: B 122 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7831 (tmtt) REVERT: B 171 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 184 ILE cc_start: 0.8426 (mt) cc_final: 0.8087 (tt) REVERT: B 242 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 257 GLU cc_start: 0.7946 (mp0) cc_final: 0.7714 (mp0) REVERT: B 260 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 339 LYS cc_start: 0.8637 (mptt) cc_final: 0.8295 (mptt) REVERT: B 346 ASP cc_start: 0.7341 (p0) cc_final: 0.7127 (p0) REVERT: B 365 MET cc_start: 0.5184 (ppp) cc_final: 0.4638 (ppp) REVERT: C 58 ILE cc_start: 0.8412 (mt) cc_final: 0.8110 (tt) REVERT: C 79 TRP cc_start: 0.8953 (m100) cc_final: 0.8638 (m100) REVERT: C 82 LYS cc_start: 0.7954 (tptt) cc_final: 0.7640 (tptt) REVERT: C 102 VAL cc_start: 0.8436 (p) cc_final: 0.7789 (t) REVERT: C 195 MET cc_start: 0.8474 (mmm) cc_final: 0.8019 (mmm) REVERT: D 74 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7492 (tm-30) REVERT: D 106 LYS cc_start: 0.8577 (mppt) cc_final: 0.8135 (mppt) REVERT: D 110 VAL cc_start: 0.7940 (t) cc_final: 0.7609 (p) REVERT: D 147 ARG cc_start: 0.8345 (mtp85) cc_final: 0.8131 (mtp-110) REVERT: D 166 SER cc_start: 0.8323 (m) cc_final: 0.8000 (t) REVERT: D 182 MET cc_start: 0.8015 (mmm) cc_final: 0.7732 (mmm) REVERT: D 186 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7727 (ttmm) REVERT: D 204 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7191 (mm-30) REVERT: D 266 MET cc_start: 0.8212 (mtt) cc_final: 0.7936 (mtp) REVERT: E 14 LYS cc_start: 0.7764 (mptt) cc_final: 0.7496 (mptt) REVERT: E 19 MET cc_start: 0.7290 (mmm) cc_final: 0.6893 (tpt) REVERT: E 80 LYS cc_start: 0.7821 (mttp) cc_final: 0.7508 (mttp) REVERT: E 88 LYS cc_start: 0.8410 (tmmt) cc_final: 0.8032 (tmmt) REVERT: E 129 MET cc_start: 0.7799 (ttm) cc_final: 0.7405 (ttm) REVERT: F 39 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7513 (mm-30) REVERT: F 70 VAL cc_start: 0.8677 (p) cc_final: 0.8440 (t) REVERT: F 110 GLU cc_start: 0.8160 (mp0) cc_final: 0.7860 (mp0) REVERT: F 163 GLU cc_start: 0.7695 (tp30) cc_final: 0.6994 (tp30) REVERT: F 167 ASN cc_start: 0.7721 (m110) cc_final: 0.7417 (m-40) outliers start: 34 outliers final: 19 residues processed: 494 average time/residue: 0.3594 time to fit residues: 238.4462 Evaluate side-chains 487 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 467 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 B residue 198 LEU 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 179 LYS Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 245 HIS 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 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 90 optimal weight: 0.0470 chunk 117 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118759 restraints weight = 21921.912| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.12 r_work: 0.3330 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15373 Z= 0.135 Angle : 0.525 10.518 20807 Z= 0.277 Chirality : 0.044 0.321 2281 Planarity : 0.004 0.051 2674 Dihedral : 6.013 88.409 2115 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.78 % Allowed : 17.46 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1863 helix: 1.57 (0.20), residues: 692 sheet: -0.24 (0.27), residues: 360 loop : 0.11 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.005 0.001 HIS D 245 PHE 0.021 0.001 PHE A 276 TYR 0.040 0.001 TYR E 74 ARG 0.006 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 728) hydrogen bonds : angle 4.53719 ( 2019) covalent geometry : bond 0.00314 (15373) covalent geometry : angle 0.52507 (20807) *********************** 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 500 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 471 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: A 94 GLU cc_start: 0.8243 (tt0) cc_final: 0.7951 (tt0) REVERT: A 123 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7787 (mtt-85) REVERT: A 128 GLU cc_start: 0.8248 (tt0) cc_final: 0.7784 (tt0) REVERT: A 178 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 229 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 230 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7799 (mtp-110) REVERT: A 255 GLN cc_start: 0.8701 (mp10) cc_final: 0.8378 (mm-40) REVERT: A 267 PHE cc_start: 0.8067 (p90) cc_final: 0.7576 (p90) REVERT: A 292 PHE cc_start: 0.7880 (t80) cc_final: 0.7153 (t80) REVERT: A 333 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.7656 (ttp80) REVERT: A 338 ASP cc_start: 0.7398 (m-30) cc_final: 0.7138 (m-30) REVERT: A 386 SER cc_start: 0.8613 (t) cc_final: 0.8266 (t) REVERT: A 406 SER cc_start: 0.8612 (m) cc_final: 0.8373 (p) REVERT: B 74 MET cc_start: -0.0088 (mmp) cc_final: -0.0348 (mmp) REVERT: B 85 MET cc_start: 0.7986 (mmp) cc_final: 0.7447 (mmp) REVERT: B 108 LEU cc_start: 0.8644 (tt) cc_final: 0.8412 (tp) REVERT: B 122 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7846 (tmtt) REVERT: B 171 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 214 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7954 (ttp80) REVERT: B 242 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 257 GLU cc_start: 0.7958 (mp0) cc_final: 0.7718 (mp0) REVERT: B 260 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: B 346 ASP cc_start: 0.7359 (p0) cc_final: 0.7154 (p0) REVERT: B 365 MET cc_start: 0.5215 (ppp) cc_final: 0.4621 (ppp) REVERT: C 58 ILE cc_start: 0.8398 (mt) cc_final: 0.8112 (tt) REVERT: C 79 TRP cc_start: 0.8954 (m100) cc_final: 0.8631 (m100) REVERT: C 82 LYS cc_start: 0.7977 (tptt) cc_final: 0.7644 (tptt) REVERT: C 195 MET cc_start: 0.8454 (mmm) cc_final: 0.7966 (mmm) REVERT: D 74 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7536 (tm-30) REVERT: D 106 LYS cc_start: 0.8567 (mppt) cc_final: 0.8119 (mppt) REVERT: D 110 VAL cc_start: 0.7961 (t) cc_final: 0.7637 (p) REVERT: D 166 SER cc_start: 0.8315 (m) cc_final: 0.8035 (t) REVERT: D 182 MET cc_start: 0.8012 (mmm) cc_final: 0.7738 (mmm) REVERT: D 186 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7717 (ttmm) REVERT: D 204 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7215 (mm-30) REVERT: D 266 MET cc_start: 0.8223 (mtt) cc_final: 0.7945 (mtp) REVERT: E 14 LYS cc_start: 0.7735 (mptt) cc_final: 0.7453 (mptt) REVERT: E 80 LYS cc_start: 0.7842 (mttp) cc_final: 0.7517 (mttp) REVERT: E 88 LYS cc_start: 0.8392 (tmmt) cc_final: 0.8016 (tmmt) REVERT: E 129 MET cc_start: 0.7762 (ttm) cc_final: 0.7557 (ttm) REVERT: F 39 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7598 (mm-30) REVERT: F 70 VAL cc_start: 0.8674 (p) cc_final: 0.8430 (t) REVERT: F 110 GLU cc_start: 0.8151 (mp0) cc_final: 0.7856 (mp0) REVERT: F 163 GLU cc_start: 0.7693 (tp30) cc_final: 0.7004 (tp30) REVERT: F 167 ASN cc_start: 0.7738 (m110) cc_final: 0.7427 (m-40) REVERT: H 196 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7778 (p) outliers start: 29 outliers final: 22 residues processed: 482 average time/residue: 0.3627 time to fit residues: 234.9056 Evaluate side-chains 490 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 465 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 219 LYS 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 230 ARG 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 196 THR 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 114 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS D 245 HIS D 278 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 = 0.3799 r_free = 0.3799 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119607 restraints weight = 21773.365| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.11 r_work: 0.3347 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15373 Z= 0.123 Angle : 0.525 10.505 20807 Z= 0.277 Chirality : 0.044 0.281 2281 Planarity : 0.004 0.058 2674 Dihedral : 5.922 86.347 2115 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.66 % Allowed : 17.95 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1863 helix: 1.57 (0.20), residues: 692 sheet: -0.17 (0.28), residues: 357 loop : 0.13 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.004 0.001 HIS F 137 PHE 0.020 0.001 PHE A 276 TYR 0.046 0.002 TYR E 74 ARG 0.013 0.001 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 728) hydrogen bonds : angle 4.50065 ( 2019) covalent geometry : bond 0.00285 (15373) covalent geometry : angle 0.52503 (20807) *********************** 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 493 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 466 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8652 (m-80) cc_final: 0.8411 (m-10) REVERT: A 79 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7204 (mtm-85) REVERT: A 93 MET cc_start: 0.8086 (mmm) cc_final: 0.7700 (mmm) REVERT: A 123 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7742 (mtt-85) REVERT: A 128 GLU cc_start: 0.8262 (tt0) cc_final: 0.7918 (tt0) REVERT: A 178 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 229 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 230 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7795 (mtp-110) REVERT: A 255 GLN cc_start: 0.8690 (mp10) cc_final: 0.8360 (mm-40) REVERT: A 267 PHE cc_start: 0.8059 (p90) cc_final: 0.7560 (p90) REVERT: A 292 PHE cc_start: 0.7873 (t80) cc_final: 0.7148 (t80) REVERT: A 333 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7641 (ttp80) REVERT: A 338 ASP cc_start: 0.7404 (m-30) cc_final: 0.7145 (m-30) REVERT: A 386 SER cc_start: 0.8597 (t) cc_final: 0.8243 (t) REVERT: A 406 SER cc_start: 0.8605 (m) cc_final: 0.8365 (p) REVERT: B 85 MET cc_start: 0.7981 (mmp) cc_final: 0.7416 (mmp) REVERT: B 108 LEU cc_start: 0.8621 (tt) cc_final: 0.8407 (tp) REVERT: B 122 LYS cc_start: 0.8258 (tmtt) cc_final: 0.7815 (tmtt) REVERT: B 171 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 184 ILE cc_start: 0.8422 (mt) cc_final: 0.8111 (tt) REVERT: B 242 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 257 GLU cc_start: 0.7951 (mp0) cc_final: 0.7718 (mp0) REVERT: B 260 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 339 LYS cc_start: 0.8515 (mptt) cc_final: 0.8172 (mptt) REVERT: B 346 ASP cc_start: 0.7338 (p0) cc_final: 0.7132 (p0) REVERT: B 365 MET cc_start: 0.5200 (ppp) cc_final: 0.4586 (ppp) REVERT: C 58 ILE cc_start: 0.8357 (mt) cc_final: 0.8081 (tt) REVERT: C 79 TRP cc_start: 0.8939 (m100) cc_final: 0.8629 (m100) REVERT: C 82 LYS cc_start: 0.8002 (tptt) cc_final: 0.7681 (tptt) REVERT: C 195 MET cc_start: 0.8425 (mmm) cc_final: 0.8024 (mmm) REVERT: C 326 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8107 (mmmt) REVERT: D 74 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 106 LYS cc_start: 0.8579 (mppt) cc_final: 0.8124 (mppt) REVERT: D 110 VAL cc_start: 0.7934 (t) cc_final: 0.7629 (p) REVERT: D 166 SER cc_start: 0.8372 (m) cc_final: 0.8087 (t) REVERT: D 182 MET cc_start: 0.8005 (mmm) cc_final: 0.7732 (mmm) REVERT: D 186 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7724 (ttmm) REVERT: D 204 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7189 (mm-30) REVERT: D 266 MET cc_start: 0.8230 (mtt) cc_final: 0.7949 (mtp) REVERT: E 14 LYS cc_start: 0.7754 (mptt) cc_final: 0.7461 (mptt) REVERT: E 80 LYS cc_start: 0.7798 (mttp) cc_final: 0.7484 (mttp) REVERT: E 88 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7995 (tmmt) REVERT: E 129 MET cc_start: 0.7795 (ttm) cc_final: 0.7585 (ttm) REVERT: F 39 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7566 (mm-30) REVERT: F 70 VAL cc_start: 0.8712 (p) cc_final: 0.8462 (t) REVERT: F 110 GLU cc_start: 0.8117 (mp0) cc_final: 0.7823 (mp0) REVERT: F 163 GLU cc_start: 0.7691 (tp30) cc_final: 0.7035 (tp30) REVERT: F 167 ASN cc_start: 0.7712 (m110) cc_final: 0.7393 (m-40) outliers start: 27 outliers final: 22 residues processed: 475 average time/residue: 0.3617 time to fit residues: 232.0507 Evaluate side-chains 483 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 459 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 162 THR 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 219 LYS 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 179 LYS Chi-restraints excluded: chain D residue 230 ARG 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 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 135 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 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** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117599 restraints weight = 21739.857| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.11 r_work: 0.3315 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15373 Z= 0.188 Angle : 0.561 10.793 20807 Z= 0.295 Chirality : 0.045 0.259 2281 Planarity : 0.004 0.052 2674 Dihedral : 6.003 85.750 2114 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.72 % Allowed : 18.07 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1863 helix: 1.54 (0.20), residues: 692 sheet: -0.24 (0.27), residues: 357 loop : 0.10 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 219 HIS 0.006 0.001 HIS F 137 PHE 0.020 0.002 PHE A 276 TYR 0.052 0.002 TYR E 74 ARG 0.013 0.001 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 728) hydrogen bonds : angle 4.56429 ( 2019) covalent geometry : bond 0.00437 (15373) covalent geometry : angle 0.56138 (20807) *********************** 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 503 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 475 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7238 (mtm-85) REVERT: A 93 MET cc_start: 0.8120 (mmm) cc_final: 0.7750 (mmm) REVERT: A 128 GLU cc_start: 0.8255 (tt0) cc_final: 0.7807 (tt0) REVERT: A 161 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7810 (mtm180) REVERT: A 230 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7790 (mtp-110) REVERT: A 240 LYS cc_start: 0.8534 (mttp) cc_final: 0.8333 (mttp) REVERT: A 255 GLN cc_start: 0.8706 (mp10) cc_final: 0.8365 (mm-40) REVERT: A 266 GLU cc_start: 0.7679 (pp20) cc_final: 0.7387 (pp20) REVERT: A 267 PHE cc_start: 0.8132 (p90) cc_final: 0.7326 (p90) REVERT: A 280 GLU cc_start: 0.8024 (tp30) cc_final: 0.7753 (tp30) REVERT: A 292 PHE cc_start: 0.7907 (t80) cc_final: 0.7173 (t80) REVERT: A 333 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.7719 (ttp80) REVERT: A 338 ASP cc_start: 0.7408 (m-30) cc_final: 0.7152 (m-30) REVERT: A 386 SER cc_start: 0.8643 (t) cc_final: 0.8281 (t) REVERT: A 406 SER cc_start: 0.8657 (m) cc_final: 0.8426 (p) REVERT: B 74 MET cc_start: -0.0208 (mmp) cc_final: -0.0825 (mmp) REVERT: B 85 MET cc_start: 0.7977 (mmp) cc_final: 0.7773 (mmp) REVERT: B 108 LEU cc_start: 0.8650 (tt) cc_final: 0.8423 (tp) REVERT: B 122 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7857 (tmtt) REVERT: B 127 MET cc_start: 0.7808 (mmp) cc_final: 0.7438 (mmp) REVERT: B 171 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 242 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 257 GLU cc_start: 0.7944 (mp0) cc_final: 0.7703 (mp0) REVERT: B 260 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 346 ASP cc_start: 0.7357 (p0) cc_final: 0.7144 (p0) REVERT: B 365 MET cc_start: 0.5216 (ppp) cc_final: 0.4569 (ppp) REVERT: C 58 ILE cc_start: 0.8391 (mt) cc_final: 0.8117 (tt) REVERT: C 79 TRP cc_start: 0.8960 (m100) cc_final: 0.8639 (m100) REVERT: C 82 LYS cc_start: 0.7970 (tptt) cc_final: 0.7661 (tptt) REVERT: C 119 VAL cc_start: 0.8727 (m) cc_final: 0.8342 (p) REVERT: C 195 MET cc_start: 0.8449 (mmm) cc_final: 0.7983 (mmm) REVERT: C 326 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8124 (mmmt) REVERT: D 13 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: D 74 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7553 (tm-30) REVERT: D 106 LYS cc_start: 0.8612 (mppt) cc_final: 0.8147 (mppt) REVERT: D 110 VAL cc_start: 0.7972 (t) cc_final: 0.7657 (p) REVERT: D 117 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8429 (ttpp) REVERT: D 166 SER cc_start: 0.8342 (m) cc_final: 0.8092 (t) REVERT: D 182 MET cc_start: 0.7957 (mmm) cc_final: 0.7691 (mmm) REVERT: D 186 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7715 (ttmm) REVERT: D 204 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 14 LYS cc_start: 0.7758 (mptt) cc_final: 0.7473 (mptt) REVERT: E 80 LYS cc_start: 0.7850 (mttp) cc_final: 0.7617 (mttp) REVERT: E 88 LYS cc_start: 0.8415 (tmmt) cc_final: 0.8050 (tmmt) REVERT: F 39 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7487 (mm-30) REVERT: F 70 VAL cc_start: 0.8691 (p) cc_final: 0.8442 (t) REVERT: F 105 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8135 (mtp85) REVERT: F 110 GLU cc_start: 0.8150 (mp0) cc_final: 0.7866 (mp0) REVERT: F 139 MET cc_start: 0.8484 (mtt) cc_final: 0.8117 (mtp) REVERT: F 163 GLU cc_start: 0.7712 (tp30) cc_final: 0.7010 (tp30) REVERT: F 167 ASN cc_start: 0.7778 (m110) cc_final: 0.7456 (m-40) outliers start: 28 outliers final: 19 residues processed: 485 average time/residue: 0.3658 time to fit residues: 239.2691 Evaluate side-chains 493 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 472 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 413 VAL Chi-restraints excluded: chain B residue 198 LEU 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 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 36 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 137 optimal weight: 0.0000 chunk 164 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119233 restraints weight = 21794.411| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.12 r_work: 0.3335 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15373 Z= 0.139 Angle : 0.552 10.799 20807 Z= 0.290 Chirality : 0.045 0.252 2281 Planarity : 0.004 0.053 2674 Dihedral : 5.908 83.548 2114 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.60 % Allowed : 18.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1863 helix: 1.55 (0.20), residues: 693 sheet: -0.20 (0.28), residues: 352 loop : 0.06 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 185 HIS 0.004 0.001 HIS F 137 PHE 0.021 0.001 PHE A 276 TYR 0.052 0.002 TYR E 74 ARG 0.012 0.001 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 728) hydrogen bonds : angle 4.53762 ( 2019) covalent geometry : bond 0.00324 (15373) covalent geometry : angle 0.55172 (20807) ********************** 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 495 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 469 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: A 93 MET cc_start: 0.8107 (mmm) cc_final: 0.7766 (mmm) REVERT: A 114 GLU cc_start: 0.8130 (pt0) cc_final: 0.7922 (pt0) REVERT: A 128 GLU cc_start: 0.8262 (tt0) cc_final: 0.7933 (tt0) REVERT: A 161 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7756 (mtm180) REVERT: A 229 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7483 (mm-30) REVERT: A 230 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: A 255 GLN cc_start: 0.8683 (mp10) cc_final: 0.8361 (mm-40) REVERT: A 266 GLU cc_start: 0.7639 (pp20) cc_final: 0.7326 (pp20) REVERT: A 267 PHE cc_start: 0.8125 (p90) cc_final: 0.7301 (p90) REVERT: A 292 PHE cc_start: 0.7877 (t80) cc_final: 0.7137 (t80) REVERT: A 333 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7632 (ttp80) REVERT: A 338 ASP cc_start: 0.7411 (m-30) cc_final: 0.7134 (m-30) REVERT: A 386 SER cc_start: 0.8610 (t) cc_final: 0.8248 (t) REVERT: A 406 SER cc_start: 0.8663 (m) cc_final: 0.8393 (p) REVERT: B 85 MET cc_start: 0.7936 (mmp) cc_final: 0.7626 (mmp) REVERT: B 108 LEU cc_start: 0.8656 (tt) cc_final: 0.8435 (tp) REVERT: B 122 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7853 (tmtt) REVERT: B 127 MET cc_start: 0.7766 (mmp) cc_final: 0.7480 (mmt) REVERT: B 171 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 184 ILE cc_start: 0.8419 (mt) cc_final: 0.8105 (tt) REVERT: B 235 LEU cc_start: 0.8501 (tt) cc_final: 0.8201 (mt) REVERT: B 242 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 257 GLU cc_start: 0.7931 (mp0) cc_final: 0.7692 (mp0) REVERT: B 260 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: B 339 LYS cc_start: 0.8534 (mptt) cc_final: 0.8203 (mptt) REVERT: B 346 ASP cc_start: 0.7352 (p0) cc_final: 0.7139 (p0) REVERT: B 365 MET cc_start: 0.5205 (ppp) cc_final: 0.4579 (ppp) REVERT: C 58 ILE cc_start: 0.8366 (mt) cc_final: 0.8077 (tt) REVERT: C 79 TRP cc_start: 0.8946 (m100) cc_final: 0.8650 (m100) REVERT: C 82 LYS cc_start: 0.7977 (tptt) cc_final: 0.7670 (tptt) REVERT: C 165 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8028 (mmmm) REVERT: C 195 MET cc_start: 0.8417 (mmm) cc_final: 0.8003 (mmm) REVERT: C 326 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8137 (mmmt) REVERT: D 74 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7541 (tm-30) REVERT: D 106 LYS cc_start: 0.8578 (mppt) cc_final: 0.8117 (mppt) REVERT: D 110 VAL cc_start: 0.7974 (t) cc_final: 0.7670 (p) REVERT: D 117 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8423 (ttpp) REVERT: D 153 TYR cc_start: 0.8616 (m-80) cc_final: 0.8360 (m-80) REVERT: D 182 MET cc_start: 0.8002 (mmm) cc_final: 0.7735 (mmm) REVERT: D 186 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7765 (ttmm) REVERT: D 204 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 14 LYS cc_start: 0.7767 (mptt) cc_final: 0.7490 (mptt) REVERT: E 80 LYS cc_start: 0.7816 (mttp) cc_final: 0.7601 (mttp) REVERT: E 88 LYS cc_start: 0.8373 (tmmt) cc_final: 0.8016 (tmmt) REVERT: F 39 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7542 (mm-30) REVERT: F 70 VAL cc_start: 0.8675 (p) cc_final: 0.8437 (t) REVERT: F 110 GLU cc_start: 0.8110 (mp0) cc_final: 0.7821 (mp0) REVERT: F 139 MET cc_start: 0.8500 (mtt) cc_final: 0.8157 (mtp) REVERT: F 163 GLU cc_start: 0.7680 (tp30) cc_final: 0.6971 (tp30) REVERT: F 167 ASN cc_start: 0.7724 (m110) cc_final: 0.7396 (m-40) outliers start: 26 outliers final: 23 residues processed: 479 average time/residue: 0.3680 time to fit residues: 237.6144 Evaluate side-chains 484 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 460 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 75 LYS 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 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 28 ASN 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 124 VAL Chi-restraints excluded: chain D residue 179 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 51 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN C 28 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119147 restraints weight = 21805.553| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.12 r_work: 0.3325 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 15373 Z= 0.191 Angle : 0.783 59.184 20807 Z= 0.457 Chirality : 0.046 0.398 2281 Planarity : 0.004 0.052 2674 Dihedral : 5.915 83.554 2114 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.66 % Allowed : 18.68 % Favored : 79.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1863 helix: 1.54 (0.20), residues: 693 sheet: -0.20 (0.28), residues: 352 loop : 0.04 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 185 HIS 0.004 0.001 HIS F 137 PHE 0.021 0.001 PHE A 276 TYR 0.046 0.002 TYR E 74 ARG 0.012 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 728) hydrogen bonds : angle 4.53795 ( 2019) covalent geometry : bond 0.00434 (15373) covalent geometry : angle 0.78342 (20807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9523.21 seconds wall clock time: 164 minutes 1.55 seconds (9841.55 seconds total)