Starting phenix.real_space_refine on Sat Aug 23 01:16:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874.map" model { file = "/net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjm_33874/08_2025/7yjm_33874_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5742 2.51 5 N 1500 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3673 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 21, 'TRANS': 449} Chain breaks: 1 Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 436 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 8895 At special positions: 0 Unit cell: (88.56, 81, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 1 15.00 O 1602 8.00 N 1500 7.00 C 5742 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 326.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 41.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 removed outlier: 3.844A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.548A pdb=" N GLU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.548A pdb=" N THR A 181 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.581A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.575A pdb=" N ILE A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.556A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 4.294A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.633A pdb=" N LEU A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.532A pdb=" N ASP A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 431' Processing helix chain 'A' and resid 468 through 477 removed outlier: 3.747A pdb=" N LEU A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.514A pdb=" N LEU B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.670A pdb=" N PHE B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.775A pdb=" N CYS B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.824A pdb=" N SER B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.703A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.532A pdb=" N ALA B 264 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.581A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.716A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 387 removed outlier: 4.055A pdb=" N GLN B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.843A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 3.717A pdb=" N LYS B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.527A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.559A pdb=" N HIS D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 4.130A pdb=" N ASP D 79 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 128 through 140 removed outlier: 4.188A pdb=" N VAL D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.922A pdb=" N GLY D 152 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 4.278A pdb=" N GLU E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 removed outlier: 3.652A pdb=" N TYR C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.579A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.626A pdb=" N LEU C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.616A pdb=" N THR A 105 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 111 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU A 433 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 112 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.456A pdb=" N THR A 152 " --> pdb=" O ILE B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.625A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 279 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 249 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASP A 281 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 251 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.729A pdb=" N ILE A 451 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.227A pdb=" N ILE B 2 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 8 " --> pdb=" O ILE B 2 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.352A pdb=" N LEU B 103 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.552A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 319 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 308 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 186 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG B 210 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 188 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE B 212 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER B 190 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 403 through 404 removed outlier: 3.781A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 735 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: 0.97 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.45: 1359 1.45 - 1.57: 4888 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 9104 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.329 1.522 -0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" C2 PLP B 501 " pdb=" C3 PLP B 501 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C4 PLP B 501 " pdb=" C5 PLP B 501 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C3 PLP B 501 " pdb=" C4 PLP B 501 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C MET B 401 " pdb=" O MET B 401 " ideal model delta sigma weight residual 1.242 1.223 0.019 9.70e-03 1.06e+04 3.98e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 11700 2.19 - 4.37: 525 4.37 - 6.56: 88 6.56 - 8.75: 7 8.75 - 10.94: 2 Bond angle restraints: 12322 Sorted by residual: angle pdb=" C GLY A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 119.84 128.25 -8.41 1.25e+00 6.40e-01 4.52e+01 angle pdb=" N LEU A 289 " pdb=" CA LEU A 289 " pdb=" C LEU A 289 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N GLU B 230 " pdb=" CA GLU B 230 " pdb=" C GLU B 230 " ideal model delta sigma weight residual 111.28 117.56 -6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" C ALA B 133 " pdb=" CA ALA B 133 " pdb=" CB ALA B 133 " ideal model delta sigma weight residual 116.54 110.57 5.97 1.15e+00 7.56e-01 2.69e+01 angle pdb=" N GLU B 253 " pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 114.75 108.51 6.24 1.26e+00 6.30e-01 2.46e+01 ... (remaining 12317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4509 17.53 - 35.06: 562 35.06 - 52.59: 270 52.59 - 70.11: 71 70.11 - 87.64: 9 Dihedral angle restraints: 5421 sinusoidal: 2185 harmonic: 3236 Sorted by residual: dihedral pdb=" CG ARG B 455 " pdb=" CD ARG B 455 " pdb=" NE ARG B 455 " pdb=" CZ ARG B 455 " ideal model delta sinusoidal sigma weight residual -90.00 -40.65 -49.35 2 1.50e+01 4.44e-03 1.23e+01 dihedral pdb=" CA ASP B 34 " pdb=" CB ASP B 34 " pdb=" CG ASP B 34 " pdb=" OD1 ASP B 34 " ideal model delta sinusoidal sigma weight residual -30.00 -88.61 58.61 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 430 " pdb=" C ASP A 430 " pdb=" N SER A 431 " pdb=" CA SER A 431 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1124 0.073 - 0.147: 211 0.147 - 0.220: 25 0.220 - 0.293: 12 0.293 - 0.367: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA TYR D 122 " pdb=" N TYR D 122 " pdb=" C TYR D 122 " pdb=" CB TYR D 122 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ASP D 13 " pdb=" N ASP D 13 " pdb=" C ASP D 13 " pdb=" CB ASP D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1371 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 225 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C MET A 225 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 225 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 226 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 58 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO E 59 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 59 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 59 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 169 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 170 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 42 2.54 - 3.13: 6336 3.13 - 3.72: 12470 3.72 - 4.31: 18193 4.31 - 4.90: 31804 Nonbonded interactions: 68845 Sorted by model distance: nonbonded pdb=" OE1 GLU A 321 " pdb=" N GLY A 322 " model vdw 1.946 3.120 nonbonded pdb=" O SER A 98 " pdb=" OG SER A 98 " model vdw 2.208 3.040 nonbonded pdb=" O PHE B 430 " pdb=" O THR B 433 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN B 215 " pdb=" ND1 HIS B 258 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP B 117 " pdb=" NH2 ARG B 366 " model vdw 2.295 3.120 ... (remaining 68840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.008 0.426 9105 Z= 0.569 Angle : 1.053 10.935 12322 Z= 0.708 Chirality : 0.061 0.367 1374 Planarity : 0.005 0.047 1544 Dihedral : 19.535 87.642 3347 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.44 % Rotamer: Outliers : 17.31 % Allowed : 9.64 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.69 (0.21), residues: 1108 helix: -3.60 (0.17), residues: 505 sheet: -1.38 (0.49), residues: 113 loop : -2.87 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 16 TYR 0.014 0.001 TYR B 406 PHE 0.020 0.001 PHE A 220 TRP 0.012 0.001 TRP B 239 HIS 0.007 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 9104) covalent geometry : angle 1.05256 (12322) hydrogen bonds : bond 0.32125 ( 260) hydrogen bonds : angle 9.72366 ( 735) Misc. bond : bond 0.42627 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 99 time to evaluate : 0.260 Fit side-chains REVERT: A 87 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: A 91 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7440 (p-80) REVERT: A 147 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.9017 (mmm160) REVERT: A 153 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8690 (mm) REVERT: A 192 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (tttp) REVERT: A 246 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: A 291 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7265 (ptm-80) REVERT: A 390 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: A 411 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 439 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7237 (mtt-85) REVERT: B 1 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.5220 (tpp) REVERT: B 31 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6621 (mtm-85) REVERT: B 47 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6883 (pt) REVERT: B 64 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: B 90 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7384 (m110) REVERT: B 118 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: B 130 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8467 (tttm) REVERT: B 437 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 29 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9078 (m) REVERT: D 72 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8776 (mtmm) REVERT: D 84 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8498 (m110) REVERT: D 100 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.8073 (ttt-90) REVERT: C 27 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8414 (tt) REVERT: C 35 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9332 (tp) REVERT: C 46 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.4344 (t80) outliers start: 167 outliers final: 100 residues processed: 238 average time/residue: 0.1114 time to fit residues: 33.8007 Evaluate side-chains 216 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 92 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 46 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 459 HIS ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.083087 restraints weight = 12349.233| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.78 r_work: 0.2670 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9105 Z= 0.135 Angle : 0.612 9.505 12322 Z= 0.324 Chirality : 0.044 0.170 1374 Planarity : 0.005 0.054 1544 Dihedral : 13.243 88.209 1561 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.60 % Favored : 93.95 % Rotamer: Outliers : 5.18 % Allowed : 17.93 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.23), residues: 1108 helix: -2.80 (0.19), residues: 517 sheet: -0.77 (0.52), residues: 110 loop : -2.22 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 241 TYR 0.016 0.001 TYR B 171 PHE 0.015 0.001 PHE B 212 TRP 0.010 0.001 TRP B 239 HIS 0.006 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9104) covalent geometry : angle 0.61165 (12322) hydrogen bonds : bond 0.04835 ( 260) hydrogen bonds : angle 4.95927 ( 735) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 0.207 Fit side-chains REVERT: A 67 GLN cc_start: 0.8464 (tp40) cc_final: 0.8253 (tp40) REVERT: A 87 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: A 246 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7681 (mtm110) REVERT: A 407 LYS cc_start: 0.7972 (tptp) cc_final: 0.7753 (tptp) REVERT: A 414 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 420 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: B 18 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 47 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7022 (pt) REVERT: B 90 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.7079 (m110) REVERT: B 375 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7784 (ttt-90) outliers start: 50 outliers final: 32 residues processed: 149 average time/residue: 0.0911 time to fit residues: 18.3188 Evaluate side-chains 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 207 GLN B 214 HIS ** B 333 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 = 0.3050 r_free = 0.3050 target = 0.101863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.080290 restraints weight = 12363.253| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.77 r_work: 0.2617 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9105 Z= 0.191 Angle : 0.605 8.989 12322 Z= 0.319 Chirality : 0.046 0.161 1374 Planarity : 0.005 0.055 1544 Dihedral : 10.290 59.899 1343 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 5.80 % Allowed : 18.65 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.24), residues: 1108 helix: -2.18 (0.21), residues: 511 sheet: -0.46 (0.53), residues: 113 loop : -2.01 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.017 0.002 TYR B 85 PHE 0.020 0.002 PHE A 220 TRP 0.010 0.001 TRP B 239 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9104) covalent geometry : angle 0.60541 (12322) hydrogen bonds : bond 0.05272 ( 260) hydrogen bonds : angle 4.67175 ( 735) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 0.262 Fit side-chains REVERT: A 67 GLN cc_start: 0.8512 (tp40) cc_final: 0.8284 (tp40) REVERT: A 86 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8974 (m) REVERT: A 153 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 246 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7750 (mtm180) REVERT: A 407 LYS cc_start: 0.7920 (tptp) cc_final: 0.7652 (tptp) REVERT: A 414 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 420 GLU cc_start: 0.8576 (tp30) cc_final: 0.8296 (tt0) REVERT: B 18 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 47 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7352 (pt) REVERT: B 98 LYS cc_start: 0.8170 (tttp) cc_final: 0.7098 (tptp) REVERT: B 177 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 374 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9171 (tp) REVERT: B 375 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7844 (ttt-90) REVERT: C 46 TYR cc_start: 0.5250 (OUTLIER) cc_final: 0.4594 (t80) outliers start: 56 outliers final: 34 residues processed: 147 average time/residue: 0.1002 time to fit residues: 19.5083 Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 46 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.093956 restraints weight = 12042.365| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.78 r_work: 0.2696 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9105 Z= 0.087 Angle : 0.493 7.744 12322 Z= 0.259 Chirality : 0.041 0.139 1374 Planarity : 0.004 0.055 1544 Dihedral : 8.792 59.403 1323 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.79 % Favored : 95.94 % Rotamer: Outliers : 4.35 % Allowed : 19.79 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.25), residues: 1108 helix: -1.53 (0.23), residues: 507 sheet: -0.27 (0.54), residues: 113 loop : -1.72 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.014 0.001 TYR B 171 PHE 0.012 0.001 PHE B 212 TRP 0.007 0.001 TRP B 239 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 9104) covalent geometry : angle 0.49259 (12322) hydrogen bonds : bond 0.03240 ( 260) hydrogen bonds : angle 4.12125 ( 735) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.377 Fit side-chains REVERT: A 67 GLN cc_start: 0.8414 (tp40) cc_final: 0.8208 (tp40) REVERT: A 86 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8939 (m) REVERT: A 246 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7613 (mtm180) REVERT: A 294 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7750 (mmt90) REVERT: A 330 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8063 (tpt170) REVERT: A 366 ASN cc_start: 0.8994 (m-40) cc_final: 0.8788 (m-40) REVERT: A 407 LYS cc_start: 0.7854 (tptp) cc_final: 0.7516 (tptp) REVERT: A 414 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7766 (t0) REVERT: B 47 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7329 (pt) REVERT: B 98 LYS cc_start: 0.8030 (tttp) cc_final: 0.6964 (tptp) REVERT: B 230 GLU cc_start: 0.7851 (tt0) cc_final: 0.7634 (mt-10) REVERT: B 374 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9137 (tp) REVERT: B 375 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7746 (ttt-90) REVERT: C 27 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8518 (tt) outliers start: 42 outliers final: 27 residues processed: 134 average time/residue: 0.1298 time to fit residues: 22.8066 Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.088684 restraints weight = 12106.952| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.78 r_work: 0.2629 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9105 Z= 0.205 Angle : 0.592 7.686 12322 Z= 0.309 Chirality : 0.047 0.163 1374 Planarity : 0.005 0.057 1544 Dihedral : 8.673 59.932 1308 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.78 % Favored : 93.95 % Rotamer: Outliers : 4.77 % Allowed : 20.10 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.25), residues: 1108 helix: -1.48 (0.22), residues: 518 sheet: -0.22 (0.54), residues: 113 loop : -1.73 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 102 TYR 0.018 0.002 TYR B 85 PHE 0.022 0.002 PHE A 220 TRP 0.008 0.001 TRP B 239 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9104) covalent geometry : angle 0.59214 (12322) hydrogen bonds : bond 0.04994 ( 260) hydrogen bonds : angle 4.39891 ( 735) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 0.398 Fit side-chains REVERT: A 86 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8932 (m) REVERT: A 153 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8604 (mm) REVERT: A 246 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7855 (mtm180) REVERT: A 294 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.7781 (mmt90) REVERT: A 407 LYS cc_start: 0.8029 (tptp) cc_final: 0.7722 (tptp) REVERT: A 414 ASP cc_start: 0.8292 (m-30) cc_final: 0.7811 (t0) REVERT: A 420 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: B 18 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 47 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7499 (pt) REVERT: B 98 LYS cc_start: 0.8267 (tttp) cc_final: 0.7185 (tptp) REVERT: B 177 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 325 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: B 374 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9202 (tp) REVERT: D 32 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8909 (mm) REVERT: C 27 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8483 (tt) outliers start: 46 outliers final: 31 residues processed: 131 average time/residue: 0.1172 time to fit residues: 20.4838 Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.083931 restraints weight = 12281.936| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.81 r_work: 0.2689 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9105 Z= 0.087 Angle : 0.484 6.685 12322 Z= 0.254 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.055 1544 Dihedral : 7.762 59.512 1298 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.88 % Favored : 95.85 % Rotamer: Outliers : 4.46 % Allowed : 20.62 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.25), residues: 1108 helix: -0.97 (0.23), residues: 512 sheet: -0.27 (0.51), residues: 125 loop : -1.56 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.017 0.001 TYR B 171 PHE 0.011 0.001 PHE B 212 TRP 0.007 0.001 TRP B 239 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9104) covalent geometry : angle 0.48445 (12322) hydrogen bonds : bond 0.03230 ( 260) hydrogen bonds : angle 3.98987 ( 735) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.353 Fit side-chains REVERT: A 86 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8905 (m) REVERT: A 225 MET cc_start: 0.8284 (mmp) cc_final: 0.8047 (mmt) REVERT: A 246 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7836 (mtm180) REVERT: A 266 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: A 294 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7721 (mmt90) REVERT: A 366 ASN cc_start: 0.9044 (m-40) cc_final: 0.8822 (m-40) REVERT: A 407 LYS cc_start: 0.7905 (tptp) cc_final: 0.7292 (tptp) REVERT: A 414 ASP cc_start: 0.8242 (m-30) cc_final: 0.7831 (t0) REVERT: B 98 LYS cc_start: 0.8065 (tttp) cc_final: 0.6978 (tptp) REVERT: B 177 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 374 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9153 (tp) REVERT: C 27 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8434 (tt) outliers start: 43 outliers final: 25 residues processed: 132 average time/residue: 0.1182 time to fit residues: 20.6359 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.0020 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.081927 restraints weight = 12398.218| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.81 r_work: 0.2653 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9105 Z= 0.138 Angle : 0.522 6.567 12322 Z= 0.273 Chirality : 0.044 0.150 1374 Planarity : 0.004 0.055 1544 Dihedral : 7.668 58.815 1292 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 3.83 % Allowed : 20.73 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.25), residues: 1108 helix: -0.78 (0.23), residues: 511 sheet: -0.14 (0.54), residues: 113 loop : -1.50 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.017 0.001 TYR B 171 PHE 0.017 0.001 PHE A 220 TRP 0.008 0.001 TRP A 204 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9104) covalent geometry : angle 0.52169 (12322) hydrogen bonds : bond 0.04015 ( 260) hydrogen bonds : angle 4.07764 ( 735) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.213 Fit side-chains REVERT: A 153 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8532 (mm) REVERT: A 246 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7811 (mtm180) REVERT: A 266 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: A 294 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7697 (mmt90) REVERT: A 366 ASN cc_start: 0.9109 (m-40) cc_final: 0.8887 (m-40) REVERT: A 407 LYS cc_start: 0.7961 (tptp) cc_final: 0.7429 (tptp) REVERT: A 414 ASP cc_start: 0.8293 (m-30) cc_final: 0.7781 (t0) REVERT: A 420 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 98 LYS cc_start: 0.8098 (tttp) cc_final: 0.7045 (tptp) REVERT: B 177 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 374 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9182 (tp) REVERT: B 375 ARG cc_start: 0.8398 (ttt-90) cc_final: 0.8092 (ttm-80) REVERT: C 27 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8499 (tt) outliers start: 37 outliers final: 25 residues processed: 129 average time/residue: 0.1071 time to fit residues: 18.1843 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.090177 restraints weight = 12070.577| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.76 r_work: 0.2689 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9105 Z= 0.090 Angle : 0.478 5.992 12322 Z= 0.250 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.053 1544 Dihedral : 7.281 58.691 1292 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.79 % Favored : 95.94 % Rotamer: Outliers : 3.63 % Allowed : 21.24 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.26), residues: 1108 helix: -0.41 (0.24), residues: 514 sheet: -0.16 (0.49), residues: 135 loop : -1.40 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.018 0.001 TYR B 171 PHE 0.012 0.001 PHE B 212 TRP 0.006 0.001 TRP C 23 HIS 0.003 0.000 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9104) covalent geometry : angle 0.47824 (12322) hydrogen bonds : bond 0.03134 ( 260) hydrogen bonds : angle 3.88454 ( 735) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.352 Fit side-chains REVERT: A 153 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (mm) REVERT: A 246 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7787 (mtm180) REVERT: A 266 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: A 294 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7211 (mmt90) REVERT: A 298 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: A 366 ASN cc_start: 0.9025 (m-40) cc_final: 0.8800 (m-40) REVERT: A 407 LYS cc_start: 0.7771 (tptp) cc_final: 0.7286 (tptp) REVERT: A 414 ASP cc_start: 0.8303 (m-30) cc_final: 0.7736 (t0) REVERT: A 420 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 98 LYS cc_start: 0.8028 (tttp) cc_final: 0.6944 (tptp) REVERT: B 177 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 306 MET cc_start: 0.8977 (tmm) cc_final: 0.8687 (ttp) REVERT: B 374 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9145 (tp) REVERT: B 375 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.7961 (ttm-80) REVERT: C 27 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8485 (tt) outliers start: 35 outliers final: 21 residues processed: 130 average time/residue: 0.1142 time to fit residues: 19.6748 Evaluate side-chains 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 0.4980 chunk 53 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.091695 restraints weight = 11971.536| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.79 r_work: 0.2684 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9105 Z= 0.120 Angle : 0.513 7.846 12322 Z= 0.266 Chirality : 0.044 0.148 1374 Planarity : 0.004 0.054 1544 Dihedral : 7.235 59.514 1290 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.32 % Allowed : 21.35 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.26), residues: 1108 helix: -0.26 (0.24), residues: 513 sheet: -0.01 (0.55), residues: 113 loop : -1.27 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.019 0.001 TYR C 26 PHE 0.016 0.001 PHE A 220 TRP 0.008 0.001 TRP A 204 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9104) covalent geometry : angle 0.51258 (12322) hydrogen bonds : bond 0.03715 ( 260) hydrogen bonds : angle 3.96613 ( 735) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.365 Fit side-chains REVERT: A 153 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 246 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7833 (mtm180) REVERT: A 266 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: A 294 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7191 (mmt90) REVERT: A 298 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: A 366 ASN cc_start: 0.9079 (m-40) cc_final: 0.8854 (m-40) REVERT: A 407 LYS cc_start: 0.7855 (tptp) cc_final: 0.7383 (tptp) REVERT: A 414 ASP cc_start: 0.8301 (m-30) cc_final: 0.7739 (t0) REVERT: A 420 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: B 18 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 98 LYS cc_start: 0.8048 (tttp) cc_final: 0.6987 (tptp) REVERT: B 177 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 374 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9166 (tp) REVERT: B 375 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8043 (ttm-80) REVERT: B 404 MET cc_start: 0.9355 (mmm) cc_final: 0.9100 (mmm) REVERT: C 27 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8508 (tt) outliers start: 32 outliers final: 20 residues processed: 125 average time/residue: 0.1237 time to fit residues: 20.4955 Evaluate side-chains 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.091834 restraints weight = 11940.767| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.81 r_work: 0.2685 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9105 Z= 0.118 Angle : 0.512 7.558 12322 Z= 0.265 Chirality : 0.043 0.148 1374 Planarity : 0.004 0.054 1544 Dihedral : 7.053 59.900 1286 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 3.42 % Allowed : 21.35 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.26), residues: 1108 helix: -0.16 (0.24), residues: 517 sheet: -0.04 (0.51), residues: 125 loop : -1.33 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.017 0.001 TYR B 171 PHE 0.015 0.001 PHE A 220 TRP 0.007 0.001 TRP B 239 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9104) covalent geometry : angle 0.51151 (12322) hydrogen bonds : bond 0.03642 ( 260) hydrogen bonds : angle 3.99312 ( 735) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.352 Fit side-chains REVERT: A 153 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 246 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7845 (mtm180) REVERT: A 266 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: A 294 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7181 (mmt90) REVERT: A 298 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: A 366 ASN cc_start: 0.9078 (m-40) cc_final: 0.8853 (m-40) REVERT: A 407 LYS cc_start: 0.7692 (tptp) cc_final: 0.7162 (tptp) REVERT: A 414 ASP cc_start: 0.8270 (m-30) cc_final: 0.7743 (t0) REVERT: A 420 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: B 18 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 98 LYS cc_start: 0.8048 (tttp) cc_final: 0.6981 (tptp) REVERT: B 177 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 374 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9162 (tp) REVERT: B 375 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8033 (ttm-80) REVERT: C 27 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8462 (tt) outliers start: 33 outliers final: 22 residues processed: 126 average time/residue: 0.1256 time to fit residues: 20.8893 Evaluate side-chains 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091205 restraints weight = 11852.311| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.79 r_work: 0.2691 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9105 Z= 0.128 Angle : 0.523 7.578 12322 Z= 0.270 Chirality : 0.044 0.150 1374 Planarity : 0.004 0.054 1544 Dihedral : 7.074 59.670 1286 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.78 % Favored : 95.04 % Rotamer: Outliers : 3.42 % Allowed : 21.45 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.26), residues: 1108 helix: -0.10 (0.24), residues: 517 sheet: 0.02 (0.54), residues: 113 loop : -1.27 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.018 0.001 TYR B 171 PHE 0.016 0.001 PHE A 220 TRP 0.008 0.001 TRP A 204 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9104) covalent geometry : angle 0.52263 (12322) hydrogen bonds : bond 0.03858 ( 260) hydrogen bonds : angle 4.01977 ( 735) Misc. bond : bond 0.00049 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.36 seconds wall clock time: 33 minutes 9.12 seconds (1989.12 seconds total)