Starting phenix.real_space_refine on Thu Jul 2 22:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2026/9mip_48300.map" } resolution = 3.4 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= 0.017 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 Mn 2 7.51 5 S 58 5.16 5 C 6766 2.51 5 N 1763 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3573 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 27, 'TRANS': 401} Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2431 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 2.17, per 1000 atoms: 0.21 Number of scatterers: 10549 At special positions: 0 Unit cell: (109.824, 116.16, 115.104, 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) Mn 2 24.99 S 58 16.00 O 1960 8.00 N 1763 7.00 C 6766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 547.8 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 2 sheets defined 75.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.511A pdb=" N ILE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.586A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.880A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 82 through 87 removed outlier: 4.345A pdb=" N HIS A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 101 through 117 removed outlier: 4.051A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.924A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.742A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.421A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.637A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 235 removed outlier: 4.497A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.912A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.637A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 312 removed outlier: 3.541A pdb=" N ARG A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 removed outlier: 4.605A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.996A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.596A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.649A pdb=" N ILE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.894A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.013A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 4.178A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 455 through 474 removed outlier: 4.144A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.639A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.591A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 529 removed outlier: 4.262A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.657A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 37 through 49 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 90 through 104 removed outlier: 4.344A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.086A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 240 through 250 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 259 through 278 removed outlier: 4.068A pdb=" N TYR B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.552A pdb=" N VAL B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 removed outlier: 3.640A pdb=" N GLU B 301 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.579A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 377 removed outlier: 6.386A pdb=" N ALA B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 383 through 401 Processing helix chain 'B' and resid 401 through 435 removed outlier: 3.607A pdb=" N PHE B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 116 through 119 removed outlier: 3.602A pdb=" N GLU C 119 " --> pdb=" O GLY C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.682A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 48 removed outlier: 6.351A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 258 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.446A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 114 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE C 82 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 289 " --> pdb=" O ALA C 273 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2050 1.33 - 1.45: 2475 1.45 - 1.57: 6167 1.57 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 10779 Sorted by residual: bond pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" N ASN B 440 " pdb=" CA ASN B 440 " ideal model delta sigma weight residual 1.463 1.489 -0.026 6.90e-03 2.10e+04 1.39e+01 bond pdb=" C GLU A 379 " pdb=" N VAL A 380 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N VAL C 256 " pdb=" CA VAL C 256 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" C LEU A 382 " pdb=" N ASN A 383 " ideal model delta sigma weight residual 1.334 1.291 0.043 1.27e-02 6.20e+03 1.17e+01 ... (remaining 10774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 11585 1.42 - 2.85: 2525 2.85 - 4.27: 469 4.27 - 5.70: 38 5.70 - 7.12: 6 Bond angle restraints: 14623 Sorted by residual: angle pdb=" CA GLY A 43 " pdb=" C GLY A 43 " pdb=" O GLY A 43 " ideal model delta sigma weight residual 122.29 117.92 4.37 8.10e-01 1.52e+00 2.91e+01 angle pdb=" C ILE C 113 " pdb=" N LEU C 114 " pdb=" CA LEU C 114 " ideal model delta sigma weight residual 122.81 116.82 5.99 1.57e+00 4.06e-01 1.46e+01 angle pdb=" CA LEU B 107 " pdb=" C LEU B 107 " pdb=" N PRO B 108 " ideal model delta sigma weight residual 118.23 121.73 -3.50 9.20e-01 1.18e+00 1.45e+01 angle pdb=" N PRO A 156 " pdb=" CA PRO A 156 " pdb=" C PRO A 156 " ideal model delta sigma weight residual 113.84 118.71 -4.87 1.30e+00 5.92e-01 1.40e+01 angle pdb=" CA GLU A 379 " pdb=" C GLU A 379 " pdb=" N VAL A 380 " ideal model delta sigma weight residual 117.07 121.34 -4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 14618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 5808 16.22 - 32.44: 569 32.44 - 48.66: 147 48.66 - 64.88: 32 64.88 - 81.10: 8 Dihedral angle restraints: 6564 sinusoidal: 2684 harmonic: 3880 Sorted by residual: dihedral pdb=" C PHE A 578 " pdb=" N PHE A 578 " pdb=" CA PHE A 578 " pdb=" CB PHE A 578 " ideal model delta harmonic sigma weight residual -122.60 -131.63 9.03 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" C THR A 281 " pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" CB THR A 281 " ideal model delta harmonic sigma weight residual -122.00 -130.66 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C PHE B 104 " pdb=" N PHE B 104 " pdb=" CA PHE B 104 " pdb=" CB PHE B 104 " ideal model delta harmonic sigma weight residual -122.60 -130.60 8.00 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 6561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 963 0.053 - 0.106: 375 0.106 - 0.159: 209 0.159 - 0.212: 97 0.212 - 0.264: 15 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA GLN C 61 " pdb=" N GLN C 61 " pdb=" C GLN C 61 " pdb=" CB GLN C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU B 316 " pdb=" N GLU B 316 " pdb=" C GLU B 316 " pdb=" CB GLU B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA THR A 281 " pdb=" N THR A 281 " pdb=" C THR A 281 " pdb=" CB THR A 281 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1656 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 163 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ILE C 163 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE C 163 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 208 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C GLY C 208 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY C 208 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP C 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 356 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C LEU A 356 " 0.047 2.00e-02 2.50e+03 pdb=" O LEU A 356 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 357 " -0.016 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 12 2.46 - 3.07: 7209 3.07 - 3.68: 16868 3.68 - 4.29: 24223 4.29 - 4.90: 39602 Nonbonded interactions: 87914 Sorted by model distance: nonbonded pdb=" OD1 ASN C 117 " pdb="MN MN C 401 " model vdw 1.847 3.060 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.070 3.060 nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 2.252 3.140 nonbonded pdb=" OG SER A 152 " pdb=" OE2 GLU A 191 " model vdw 2.253 3.040 nonbonded pdb=" O LEU B 305 " pdb=" OH TYR B 349 " model vdw 2.348 3.040 ... (remaining 87909 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: 1.150 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.010 0.047 10779 Z= 0.750 Angle : 1.190 7.122 14623 Z= 0.927 Chirality : 0.079 0.264 1659 Planarity : 0.005 0.059 1877 Dihedral : 14.147 81.099 4036 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % 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 are not related in a simple way. whole: 0.60 (0.24), residues: 1304 helix: 0.86 (0.18), residues: 893 sheet: -0.72 (0.78), residues: 41 loop : -0.38 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.017 0.001 TYR A 261 PHE 0.029 0.001 PHE A 54 TRP 0.023 0.002 TRP A 450 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.75 (10779) covalent geometry : angle 1.19049 / 0.93 (14623) hydrogen bonds : bond 0.18801 / 12.46 ( 624) hydrogen bonds : angle 6.14429 / 4.48 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.7516 (m-10) cc_final: 0.7246 (m-80) REVERT: A 106 ASP cc_start: 0.9325 (m-30) cc_final: 0.9065 (m-30) REVERT: A 245 MET cc_start: 0.9087 (mmp) cc_final: 0.8619 (mmp) REVERT: A 323 MET cc_start: 0.9202 (mtm) cc_final: 0.8926 (mmm) REVERT: A 356 LEU cc_start: 0.9494 (mt) cc_final: 0.9138 (mt) REVERT: A 379 GLU cc_start: 0.8899 (mp0) cc_final: 0.8518 (mp0) REVERT: B 65 TRP cc_start: 0.8147 (m-10) cc_final: 0.7933 (m-10) REVERT: B 356 MET cc_start: 0.8772 (mmm) cc_final: 0.8330 (mmm) REVERT: B 391 TYR cc_start: 0.7420 (m-10) cc_final: 0.7080 (m-80) REVERT: B 398 MET cc_start: 0.9242 (ptm) cc_final: 0.9012 (ppp) REVERT: B 399 GLU cc_start: 0.9599 (tt0) cc_final: 0.9157 (mt-10) REVERT: B 423 MET cc_start: 0.9438 (mmt) cc_final: 0.9213 (ptt) REVERT: C 195 MET cc_start: 0.8763 (mtm) cc_final: 0.8435 (ttm) REVERT: C 196 CYS cc_start: 0.8131 (t) cc_final: 0.7625 (t) REVERT: C 275 ILE cc_start: 0.8552 (mt) cc_final: 0.8198 (mm) REVERT: C 277 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8556 (mm-30) REVERT: C 284 TYR cc_start: 0.8697 (p90) cc_final: 0.8237 (p90) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1044 time to fit residues: 23.6999 Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 203 GLN B 297 HIS B 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.069958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053341 restraints weight = 48260.616| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 5.24 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10779 Z= 0.126 Angle : 0.599 8.398 14623 Z= 0.301 Chirality : 0.041 0.147 1659 Planarity : 0.004 0.043 1877 Dihedral : 3.924 32.816 1415 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.53 % Allowed : 14.57 % Favored : 83.90 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1304 helix: 1.63 (0.17), residues: 899 sheet: -0.89 (0.72), residues: 48 loop : 0.20 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 398 TYR 0.019 0.001 TYR A 456 PHE 0.024 0.001 PHE A 54 TRP 0.014 0.001 TRP A 450 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (10779) covalent geometry : angle 0.59889 / 0.30 (14623) hydrogen bonds : bond 0.04595 / 3.11 ( 624) hydrogen bonds : angle 4.52857 / 3.20 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9425 (mt) cc_final: 0.9158 (tp) REVERT: A 424 ILE cc_start: 0.9585 (mt) cc_final: 0.9249 (tt) REVERT: A 427 MET cc_start: 0.9402 (tpt) cc_final: 0.9061 (tpp) REVERT: A 521 MET cc_start: 0.8115 (ptt) cc_final: 0.7914 (ptt) REVERT: B 65 TRP cc_start: 0.8363 (m-10) cc_final: 0.8118 (m-10) REVERT: B 94 GLU cc_start: 0.8933 (mp0) cc_final: 0.8533 (mp0) REVERT: B 103 MET cc_start: 0.8914 (mmt) cc_final: 0.8696 (mmt) REVERT: B 105 ARG cc_start: 0.8061 (pmt-80) cc_final: 0.7703 (pmt-80) REVERT: B 356 MET cc_start: 0.8724 (mmm) cc_final: 0.8227 (mmm) REVERT: B 391 TYR cc_start: 0.7412 (m-10) cc_final: 0.7166 (m-80) REVERT: B 398 MET cc_start: 0.9327 (ptm) cc_final: 0.8984 (tmm) REVERT: B 399 GLU cc_start: 0.9644 (tt0) cc_final: 0.9327 (pt0) REVERT: C 83 MET cc_start: 0.6474 (ppp) cc_final: 0.6141 (ppp) REVERT: C 195 MET cc_start: 0.8717 (mtm) cc_final: 0.8467 (ttm) REVERT: C 196 CYS cc_start: 0.8068 (t) cc_final: 0.7764 (t) outliers start: 18 outliers final: 7 residues processed: 118 average time/residue: 0.1046 time to fit residues: 17.7876 Evaluate side-chains 96 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 135 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN A 360 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049685 restraints weight = 49349.004| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 5.16 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10779 Z= 0.181 Angle : 0.621 7.465 14623 Z= 0.309 Chirality : 0.041 0.149 1659 Planarity : 0.004 0.039 1877 Dihedral : 4.025 27.152 1415 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.64 % Allowed : 14.14 % Favored : 83.22 % 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 are not related in a simple way. whole: 1.90 (0.24), residues: 1304 helix: 1.83 (0.18), residues: 904 sheet: -0.90 (0.64), residues: 58 loop : 0.28 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 398 TYR 0.015 0.001 TYR A 261 PHE 0.028 0.002 PHE A 76 TRP 0.011 0.001 TRP B 131 HIS 0.005 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (10779) covalent geometry : angle 0.62140 / 0.31 (14623) hydrogen bonds : bond 0.04161 / 2.81 ( 624) hydrogen bonds : angle 4.35731 / 3.07 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9134 (mp0) cc_final: 0.8737 (mp0) REVERT: A 356 LEU cc_start: 0.9492 (mt) cc_final: 0.9282 (tp) REVERT: A 427 MET cc_start: 0.9429 (tpt) cc_final: 0.9044 (tpp) REVERT: B 65 TRP cc_start: 0.8360 (m-10) cc_final: 0.7923 (m-10) REVERT: B 76 MET cc_start: 0.9399 (mmm) cc_final: 0.9129 (mmm) REVERT: B 94 GLU cc_start: 0.9017 (mp0) cc_final: 0.8637 (mp0) REVERT: B 274 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8359 (t80) REVERT: B 356 MET cc_start: 0.8709 (mmm) cc_final: 0.8238 (mmm) REVERT: B 391 TYR cc_start: 0.7577 (m-10) cc_final: 0.7190 (m-80) REVERT: B 398 MET cc_start: 0.9336 (ptm) cc_final: 0.9108 (tmm) REVERT: B 399 GLU cc_start: 0.9639 (tt0) cc_final: 0.9438 (pt0) REVERT: C 85 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: C 87 VAL cc_start: 0.9068 (m) cc_final: 0.8643 (p) REVERT: C 195 MET cc_start: 0.8834 (mtm) cc_final: 0.8608 (ttm) REVERT: C 196 CYS cc_start: 0.8114 (t) cc_final: 0.7830 (t) outliers start: 31 outliers final: 13 residues processed: 114 average time/residue: 0.0963 time to fit residues: 16.1099 Evaluate side-chains 103 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.066101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049237 restraints weight = 49534.727| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 5.11 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10779 Z= 0.153 Angle : 0.607 9.739 14623 Z= 0.296 Chirality : 0.041 0.199 1659 Planarity : 0.004 0.040 1877 Dihedral : 4.016 23.180 1415 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.30 % Allowed : 15.08 % Favored : 82.62 % 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 are not related in a simple way. whole: 1.88 (0.24), residues: 1304 helix: 1.86 (0.18), residues: 903 sheet: -1.07 (0.64), residues: 58 loop : 0.14 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.012 0.001 TYR A 261 PHE 0.022 0.001 PHE A 76 TRP 0.008 0.001 TRP C 250 HIS 0.005 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (10779) covalent geometry : angle 0.60706 / 0.30 (14623) hydrogen bonds : bond 0.03748 / 2.53 ( 624) hydrogen bonds : angle 4.25502 / 3.01 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9116 (mp0) cc_final: 0.8713 (mp0) REVERT: A 356 LEU cc_start: 0.9507 (mt) cc_final: 0.9180 (tp) REVERT: A 427 MET cc_start: 0.9430 (tpt) cc_final: 0.9048 (tpp) REVERT: A 499 MET cc_start: 0.8809 (mmp) cc_final: 0.8277 (mmp) REVERT: B 65 TRP cc_start: 0.8297 (m-10) cc_final: 0.7842 (m-10) REVERT: B 76 MET cc_start: 0.9426 (mmm) cc_final: 0.9174 (mmt) REVERT: B 94 GLU cc_start: 0.9000 (mp0) cc_final: 0.8617 (mp0) REVERT: B 274 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8425 (t80) REVERT: B 303 MET cc_start: 0.9412 (mtm) cc_final: 0.9195 (mtm) REVERT: B 356 MET cc_start: 0.8754 (mmm) cc_final: 0.8246 (mmm) REVERT: B 391 TYR cc_start: 0.7680 (m-10) cc_final: 0.7330 (m-80) REVERT: B 398 MET cc_start: 0.9311 (ptm) cc_final: 0.9031 (tmm) REVERT: B 399 GLU cc_start: 0.9667 (tt0) cc_final: 0.9426 (pt0) REVERT: C 85 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.5269 (p0) REVERT: C 87 VAL cc_start: 0.9143 (m) cc_final: 0.8737 (p) REVERT: C 195 MET cc_start: 0.8913 (mtm) cc_final: 0.8679 (ttm) REVERT: C 196 CYS cc_start: 0.8053 (t) cc_final: 0.7761 (t) outliers start: 27 outliers final: 15 residues processed: 111 average time/residue: 0.0921 time to fit residues: 14.9711 Evaluate side-chains 104 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050230 restraints weight = 48726.985| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 5.13 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10779 Z= 0.111 Angle : 0.595 11.226 14623 Z= 0.286 Chirality : 0.040 0.221 1659 Planarity : 0.004 0.040 1877 Dihedral : 3.957 19.347 1415 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.96 % Allowed : 15.84 % Favored : 82.20 % 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 are not related in a simple way. whole: 1.86 (0.24), residues: 1304 helix: 1.81 (0.18), residues: 906 sheet: -1.06 (0.63), residues: 58 loop : 0.22 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.012 0.001 TYR A 261 PHE 0.020 0.001 PHE A 538 TRP 0.011 0.001 TRP C 250 HIS 0.004 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10779) covalent geometry : angle 0.59538 / 0.29 (14623) hydrogen bonds : bond 0.03401 / 2.30 ( 624) hydrogen bonds : angle 4.10814 / 2.91 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9098 (mp0) cc_final: 0.8719 (mp0) REVERT: A 427 MET cc_start: 0.9406 (tpt) cc_final: 0.9141 (tpp) REVERT: A 499 MET cc_start: 0.8728 (mmp) cc_final: 0.8274 (mmp) REVERT: B 65 TRP cc_start: 0.8220 (m-10) cc_final: 0.7737 (m-10) REVERT: B 76 MET cc_start: 0.9391 (mmm) cc_final: 0.9135 (mmt) REVERT: B 94 GLU cc_start: 0.8861 (mp0) cc_final: 0.8607 (mp0) REVERT: B 274 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 356 MET cc_start: 0.8772 (mmm) cc_final: 0.8301 (mmm) REVERT: B 375 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: B 391 TYR cc_start: 0.7626 (m-10) cc_final: 0.7315 (m-80) REVERT: B 398 MET cc_start: 0.9276 (ptm) cc_final: 0.8968 (tmm) REVERT: B 399 GLU cc_start: 0.9667 (tt0) cc_final: 0.9415 (pt0) REVERT: C 85 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6606 (p0) REVERT: C 87 VAL cc_start: 0.9162 (m) cc_final: 0.8760 (p) REVERT: C 191 HIS cc_start: 0.9172 (m-70) cc_final: 0.8915 (m-70) REVERT: C 195 MET cc_start: 0.8932 (mtm) cc_final: 0.8657 (ttm) REVERT: C 196 CYS cc_start: 0.8038 (t) cc_final: 0.7742 (t) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 0.0952 time to fit residues: 15.1227 Evaluate side-chains 98 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.050416 restraints weight = 48906.724| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.16 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10779 Z= 0.105 Angle : 0.592 12.383 14623 Z= 0.281 Chirality : 0.039 0.236 1659 Planarity : 0.004 0.040 1877 Dihedral : 3.890 19.190 1415 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.79 % Allowed : 16.01 % Favored : 82.20 % 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 are not related in a simple way. whole: 1.87 (0.24), residues: 1304 helix: 1.81 (0.18), residues: 906 sheet: -0.95 (0.64), residues: 58 loop : 0.25 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.010 0.001 TYR A 261 PHE 0.020 0.001 PHE A 538 TRP 0.009 0.001 TRP C 250 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10779) covalent geometry : angle 0.59184 / 0.28 (14623) hydrogen bonds : bond 0.03214 / 2.19 ( 624) hydrogen bonds : angle 4.05680 / 2.87 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9073 (mp0) cc_final: 0.8695 (mp0) REVERT: A 427 MET cc_start: 0.9430 (tpt) cc_final: 0.9174 (tpp) REVERT: B 65 TRP cc_start: 0.8177 (m-10) cc_final: 0.7655 (m-10) REVERT: B 76 MET cc_start: 0.9381 (mmm) cc_final: 0.9113 (mmt) REVERT: B 94 GLU cc_start: 0.8864 (mp0) cc_final: 0.8594 (mp0) REVERT: B 274 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8344 (t80) REVERT: B 324 MET cc_start: 0.8646 (pmm) cc_final: 0.8368 (pmm) REVERT: B 356 MET cc_start: 0.8778 (mmm) cc_final: 0.8287 (mmm) REVERT: B 375 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: B 391 TYR cc_start: 0.7633 (m-10) cc_final: 0.7386 (m-80) REVERT: B 398 MET cc_start: 0.9279 (ptm) cc_final: 0.8915 (tmm) REVERT: B 399 GLU cc_start: 0.9659 (tt0) cc_final: 0.9391 (pt0) REVERT: C 85 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.6681 (p0) REVERT: C 87 VAL cc_start: 0.9169 (m) cc_final: 0.8746 (p) REVERT: C 191 HIS cc_start: 0.9172 (m-70) cc_final: 0.8914 (m-70) REVERT: C 196 CYS cc_start: 0.8077 (t) cc_final: 0.7725 (t) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.0865 time to fit residues: 14.5587 Evaluate side-chains 105 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.066862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049994 restraints weight = 48686.519| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.14 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10779 Z= 0.114 Angle : 0.620 19.544 14623 Z= 0.288 Chirality : 0.039 0.156 1659 Planarity : 0.004 0.039 1877 Dihedral : 3.870 20.499 1415 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.79 % Allowed : 16.44 % Favored : 81.77 % 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 are not related in a simple way. whole: 1.88 (0.24), residues: 1304 helix: 1.82 (0.18), residues: 906 sheet: -0.81 (0.65), residues: 58 loop : 0.21 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 398 TYR 0.010 0.001 TYR A 261 PHE 0.019 0.001 PHE A 538 TRP 0.018 0.001 TRP A 450 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10779) covalent geometry : angle 0.62041 / 0.29 (14623) hydrogen bonds : bond 0.03245 / 2.21 ( 624) hydrogen bonds : angle 4.06307 / 2.88 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9047 (mp0) cc_final: 0.8669 (mp0) REVERT: A 424 ILE cc_start: 0.9665 (mt) cc_final: 0.9287 (tt) REVERT: A 427 MET cc_start: 0.9434 (tpt) cc_final: 0.9189 (tpp) REVERT: A 499 MET cc_start: 0.8520 (mmp) cc_final: 0.8174 (mmp) REVERT: B 65 TRP cc_start: 0.8145 (m-10) cc_final: 0.7640 (m-10) REVERT: B 94 GLU cc_start: 0.8877 (mp0) cc_final: 0.8596 (mp0) REVERT: B 274 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8345 (t80) REVERT: B 303 MET cc_start: 0.9365 (mtm) cc_final: 0.9133 (mtm) REVERT: B 324 MET cc_start: 0.8680 (pmm) cc_final: 0.8423 (pmm) REVERT: B 356 MET cc_start: 0.8778 (mmm) cc_final: 0.8274 (mmm) REVERT: B 375 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: B 391 TYR cc_start: 0.7632 (m-10) cc_final: 0.7386 (m-80) REVERT: B 398 MET cc_start: 0.9283 (ptm) cc_final: 0.8906 (tmm) REVERT: B 399 GLU cc_start: 0.9645 (tt0) cc_final: 0.9375 (pt0) REVERT: B 413 LYS cc_start: 0.9674 (pttm) cc_final: 0.9425 (mmtt) REVERT: C 85 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.6587 (p0) REVERT: C 87 VAL cc_start: 0.9206 (m) cc_final: 0.8779 (p) REVERT: C 191 HIS cc_start: 0.9143 (m-70) cc_final: 0.8889 (m-70) REVERT: C 196 CYS cc_start: 0.8058 (t) cc_final: 0.7689 (t) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 0.0890 time to fit residues: 14.1998 Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048926 restraints weight = 48925.587| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 5.11 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10779 Z= 0.146 Angle : 0.656 20.186 14623 Z= 0.308 Chirality : 0.040 0.179 1659 Planarity : 0.004 0.053 1877 Dihedral : 3.929 20.616 1415 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 16.61 % Favored : 81.69 % 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 are not related in a simple way. whole: 1.87 (0.24), residues: 1304 helix: 1.83 (0.18), residues: 905 sheet: -0.76 (0.67), residues: 53 loop : 0.12 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 398 TYR 0.010 0.001 TYR B 158 PHE 0.018 0.001 PHE A 538 TRP 0.023 0.001 TRP A 450 HIS 0.003 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10779) covalent geometry : angle 0.65639 / 0.31 (14623) hydrogen bonds : bond 0.03417 / 2.31 ( 624) hydrogen bonds : angle 4.16478 / 2.95 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8824 (m-30) cc_final: 0.8452 (p0) REVERT: A 269 GLU cc_start: 0.9043 (mp0) cc_final: 0.8502 (mp0) REVERT: A 427 MET cc_start: 0.9428 (tpt) cc_final: 0.9203 (tpp) REVERT: A 499 MET cc_start: 0.8580 (mmp) cc_final: 0.8287 (mmp) REVERT: B 65 TRP cc_start: 0.8178 (m-10) cc_final: 0.7663 (m-10) REVERT: B 76 MET cc_start: 0.9591 (mmt) cc_final: 0.9230 (mmm) REVERT: B 94 GLU cc_start: 0.8898 (mp0) cc_final: 0.8612 (mp0) REVERT: B 274 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 303 MET cc_start: 0.9352 (mtm) cc_final: 0.9128 (mtm) REVERT: B 324 MET cc_start: 0.8720 (pmm) cc_final: 0.8453 (pmm) REVERT: B 356 MET cc_start: 0.8831 (mmm) cc_final: 0.8431 (mmm) REVERT: B 375 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: B 391 TYR cc_start: 0.7657 (m-10) cc_final: 0.7401 (m-80) REVERT: B 398 MET cc_start: 0.9307 (ptm) cc_final: 0.8925 (tmm) REVERT: B 399 GLU cc_start: 0.9657 (tt0) cc_final: 0.9393 (pt0) REVERT: C 85 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: C 191 HIS cc_start: 0.9127 (m-70) cc_final: 0.8873 (m-70) REVERT: C 196 CYS cc_start: 0.7860 (t) cc_final: 0.7497 (t) REVERT: C 259 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9240 (mm) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.0848 time to fit residues: 13.5429 Evaluate side-chains 100 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049962 restraints weight = 48642.008| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.17 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10779 Z= 0.109 Angle : 0.659 19.566 14623 Z= 0.309 Chirality : 0.041 0.310 1659 Planarity : 0.004 0.041 1877 Dihedral : 3.941 20.333 1415 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.36 % Allowed : 17.55 % Favored : 81.09 % 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 are not related in a simple way. whole: 1.74 (0.24), residues: 1304 helix: 1.73 (0.18), residues: 917 sheet: -0.72 (0.65), residues: 58 loop : 0.02 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 398 TYR 0.010 0.001 TYR A 426 PHE 0.020 0.001 PHE A 538 TRP 0.018 0.001 TRP A 450 HIS 0.002 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10779) covalent geometry : angle 0.65868 / 0.31 (14623) hydrogen bonds : bond 0.03140 / 2.13 ( 624) hydrogen bonds : angle 4.10415 / 2.92 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.9037 (mmp) cc_final: 0.8682 (mmp) REVERT: A 269 GLU cc_start: 0.9033 (mp0) cc_final: 0.8493 (mp0) REVERT: A 427 MET cc_start: 0.9423 (tpt) cc_final: 0.9186 (tpp) REVERT: A 499 MET cc_start: 0.8514 (mmp) cc_final: 0.8206 (mmp) REVERT: A 521 MET cc_start: 0.7866 (ptt) cc_final: 0.7440 (ptt) REVERT: B 65 TRP cc_start: 0.8122 (m-10) cc_final: 0.7575 (m-10) REVERT: B 76 MET cc_start: 0.9539 (mmt) cc_final: 0.9178 (mmm) REVERT: B 94 GLU cc_start: 0.8868 (mp0) cc_final: 0.8578 (mp0) REVERT: B 274 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8417 (t80) REVERT: B 303 MET cc_start: 0.9357 (mtm) cc_final: 0.9109 (mtm) REVERT: B 324 MET cc_start: 0.8732 (pmm) cc_final: 0.8413 (pmm) REVERT: B 356 MET cc_start: 0.8812 (mmm) cc_final: 0.8392 (mmm) REVERT: B 375 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: B 391 TYR cc_start: 0.7644 (m-10) cc_final: 0.7390 (m-80) REVERT: B 398 MET cc_start: 0.9302 (ptm) cc_final: 0.8921 (tmm) REVERT: B 399 GLU cc_start: 0.9645 (tt0) cc_final: 0.9361 (pt0) REVERT: C 85 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.5319 (p0) REVERT: C 191 HIS cc_start: 0.9149 (m-70) cc_final: 0.8935 (m-70) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.0810 time to fit residues: 12.5700 Evaluate side-chains 97 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050097 restraints weight = 48670.032| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.13 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10779 Z= 0.111 Angle : 0.675 18.869 14623 Z= 0.313 Chirality : 0.042 0.387 1659 Planarity : 0.004 0.052 1877 Dihedral : 3.935 20.380 1415 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.19 % Allowed : 17.72 % Favored : 81.09 % 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 are not related in a simple way. whole: 1.68 (0.24), residues: 1304 helix: 1.69 (0.18), residues: 916 sheet: -0.69 (0.65), residues: 58 loop : -0.02 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 398 TYR 0.010 0.001 TYR A 426 PHE 0.021 0.001 PHE A 538 TRP 0.025 0.001 TRP A 450 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10779) covalent geometry : angle 0.67487 / 0.31 (14623) hydrogen bonds : bond 0.03123 / 2.11 ( 624) hydrogen bonds : angle 4.11933 / 2.93 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8923 (mmp) cc_final: 0.8474 (mmp) REVERT: A 269 GLU cc_start: 0.9047 (mp0) cc_final: 0.8507 (mp0) REVERT: A 427 MET cc_start: 0.9423 (tpt) cc_final: 0.9223 (tpp) REVERT: A 499 MET cc_start: 0.8545 (mmp) cc_final: 0.8236 (mmp) REVERT: A 521 MET cc_start: 0.7852 (ptt) cc_final: 0.7421 (ptt) REVERT: B 65 TRP cc_start: 0.8119 (m-10) cc_final: 0.7576 (m-10) REVERT: B 76 MET cc_start: 0.9533 (mmt) cc_final: 0.9174 (mmm) REVERT: B 94 GLU cc_start: 0.8874 (mp0) cc_final: 0.8587 (mp0) REVERT: B 274 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8402 (t80) REVERT: B 324 MET cc_start: 0.8759 (pmm) cc_final: 0.8451 (pmm) REVERT: B 375 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: B 391 TYR cc_start: 0.7619 (m-10) cc_final: 0.7392 (m-80) REVERT: B 398 MET cc_start: 0.9307 (ptm) cc_final: 0.8895 (tmm) REVERT: C 85 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.6328 (p0) REVERT: C 191 HIS cc_start: 0.9195 (m-70) cc_final: 0.8972 (m-70) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.0823 time to fit residues: 12.8571 Evaluate side-chains 97 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050208 restraints weight = 48651.689| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.17 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10779 Z= 0.108 Angle : 0.667 19.044 14623 Z= 0.308 Chirality : 0.040 0.235 1659 Planarity : 0.004 0.049 1877 Dihedral : 3.918 20.796 1415 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.28 % Allowed : 17.89 % Favored : 80.83 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1304 helix: 1.69 (0.18), residues: 915 sheet: -0.75 (0.65), residues: 58 loop : -0.07 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.009 0.001 TYR A 261 PHE 0.020 0.001 PHE A 538 TRP 0.014 0.001 TRP A 450 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10779) covalent geometry : angle 0.66656 / 0.31 (14623) hydrogen bonds : bond 0.03064 / 2.08 ( 624) hydrogen bonds : angle 4.09872 / 2.92 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.56 seconds wall clock time: 32 minutes 40.04 seconds (1960.04 seconds total)