Starting phenix.real_space_refine on Wed Sep 17 17:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mf5_48224/09_2025/9mf5_48224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mf5_48224/09_2025/9mf5_48224.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/9mf5_48224/09_2025/9mf5_48224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mf5_48224/09_2025/9mf5_48224.map" model { file = "/net/cci-nas-00/data/ceres_data/9mf5_48224/09_2025/9mf5_48224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mf5_48224/09_2025/9mf5_48224.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= 0.019 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 54 5.16 5 C 6407 2.51 5 N 1677 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9993 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4493 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 553} Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3053 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 23, 'TRANS': 342} Chain: "C" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2445 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.36, per 1000 atoms: 0.24 Number of scatterers: 9993 At special positions: 0 Unit cell: (103.684, 107.916, 116.38, 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 54 16.00 O 1853 8.00 N 1677 7.00 C 6407 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: 0.97 Conformation dependent library (CDL) restraints added in 350.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 77.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 87 through 92 removed outlier: 4.315A pdb=" N LEU A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 5.277A pdb=" N HIS A 99 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.530A pdb=" N VAL A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.893A pdb=" N GLN A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.776A pdb=" N ARG A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.650A pdb=" N CYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 190 through 208 removed outlier: 4.598A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.550A pdb=" N LEU A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 247 removed outlier: 4.153A pdb=" N LEU A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.817A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU A 253 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.513A pdb=" N GLU A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.718A pdb=" N ARG A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 295 Proline residue: A 288 - end of helix removed outlier: 3.740A pdb=" N ASN A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 307 through 324 removed outlier: 4.751A pdb=" N LYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 4.853A pdb=" N GLU A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.874A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.625A pdb=" N LYS A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.264A pdb=" N THR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.538A pdb=" N LEU A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.812A pdb=" N ASN A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 424 removed outlier: 4.286A pdb=" N VAL A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N ARG A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 428 through 447 removed outlier: 3.533A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 467 through 502 removed outlier: 6.598A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N GLU A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.700A pdb=" N ALA A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 542 removed outlier: 3.595A pdb=" N ARG A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLU A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 528 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Proline residue: A 535 - end of helix removed outlier: 3.979A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 Processing helix chain 'A' and resid 564 through 581 removed outlier: 4.483A pdb=" N LYS A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.501A pdb=" N GLN A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 62 through 83 Processing helix chain 'B' and resid 90 through 104 removed outlier: 4.254A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 130 through 147 removed outlier: 4.313A pdb=" N LEU B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.568A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B 158 " --> pdb=" O ILE B 154 " (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 250 through 255 removed outlier: 3.938A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 259 through 278 removed outlier: 4.161A 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 Processing helix chain 'B' and resid 297 through 313 Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.858A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.132A 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 361 removed outlier: 3.923A pdb=" N ASP B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 378 Proline residue: B 368 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 383 through 401 removed outlier: 3.539A pdb=" N ASN B 401 " --> pdb=" O PHE B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.609A pdb=" N GLU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 127 through 138 removed outlier: 4.615A pdb=" N ASP C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.673A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 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 45 through 48 removed outlier: 5.892A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.711A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1749 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: 1.60 Time building geometry restraints manager: 1.27 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: 2149 1.33 - 1.45: 2137 1.45 - 1.57: 5833 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 10202 Sorted by residual: bond pdb=" C ASN B 401 " pdb=" N GLN B 402 " ideal model delta sigma weight residual 1.330 1.277 0.052 1.32e-02 5.74e+03 1.58e+01 bond pdb=" C GLN C 162 " pdb=" N ILE C 163 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.27e-02 6.20e+03 1.46e+01 bond pdb=" C VAL A 360 " pdb=" N ILE A 361 " ideal model delta sigma weight residual 1.333 1.287 0.047 1.24e-02 6.50e+03 1.43e+01 bond pdb=" C PRO A 258 " pdb=" N THR A 259 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.31e-02 5.83e+03 1.42e+01 bond pdb=" C VAL A 392 " pdb=" N ARG A 393 " ideal model delta sigma weight residual 1.334 1.287 0.047 1.27e-02 6.20e+03 1.37e+01 ... (remaining 10197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11453 1.38 - 2.77: 1889 2.77 - 4.15: 430 4.15 - 5.53: 59 5.53 - 6.92: 6 Bond angle restraints: 13837 Sorted by residual: angle pdb=" N PRO A 103 " pdb=" CA PRO A 103 " pdb=" C PRO A 103 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" O PRO A 258 " pdb=" C PRO A 258 " pdb=" N THR A 259 " ideal model delta sigma weight residual 122.23 127.02 -4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" N ASP C 175 " pdb=" CA ASP C 175 " pdb=" C ASP C 175 " ideal model delta sigma weight residual 113.43 108.41 5.02 1.26e+00 6.30e-01 1.59e+01 angle pdb=" N ASN B 219 " pdb=" CA ASN B 219 " pdb=" C ASN B 219 " ideal model delta sigma weight residual 114.31 109.17 5.14 1.29e+00 6.01e-01 1.59e+01 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 121.57 118.12 3.45 8.70e-01 1.32e+00 1.58e+01 ... (remaining 13832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5531 17.79 - 35.58: 512 35.58 - 53.37: 133 53.37 - 71.16: 19 71.16 - 88.94: 11 Dihedral angle restraints: 6206 sinusoidal: 2537 harmonic: 3669 Sorted by residual: dihedral pdb=" C ASN A 293 " pdb=" N ASN A 293 " pdb=" CA ASN A 293 " pdb=" CB ASN A 293 " ideal model delta harmonic sigma weight residual -122.60 -132.17 9.57 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ASN B 206 " pdb=" N ASN B 206 " pdb=" CA ASN B 206 " pdb=" CB ASN B 206 " ideal model delta harmonic sigma weight residual -122.60 -131.67 9.07 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C THR B 184 " pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" CB THR B 184 " ideal model delta harmonic sigma weight residual -122.00 -130.61 8.61 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 6203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1077 0.062 - 0.125: 323 0.125 - 0.187: 134 0.187 - 0.249: 37 0.249 - 0.312: 4 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA ASN A 293 " pdb=" N ASN A 293 " pdb=" C ASN A 293 " pdb=" CB ASN A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1572 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 164 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C PHE C 164 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE C 164 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS C 165 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 156 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C LYS B 156 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS B 156 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 157 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 294 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C ASP A 294 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP A 294 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 295 " -0.017 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 7974 3.12 - 3.72: 16951 3.72 - 4.31: 23081 4.31 - 4.90: 37241 Nonbonded interactions: 85266 Sorted by model distance: nonbonded pdb=" OD1 ASN C 117 " pdb="MN MN C 402 " model vdw 1.942 2.320 nonbonded pdb=" CD2 HIS C 241 " pdb="MN MN C 402 " model vdw 2.057 2.540 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.141 2.320 nonbonded pdb=" OD2 ASP C 57 " pdb="MN MN C 401 " model vdw 2.230 2.320 nonbonded pdb=" NE2 HIS C 59 " pdb="MN MN C 401 " model vdw 2.331 2.400 ... (remaining 85261 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: 1.030 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.390 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 0.052 10202 Z= 0.646 Angle : 1.092 6.917 13837 Z= 0.827 Chirality : 0.074 0.312 1575 Planarity : 0.004 0.033 1778 Dihedral : 15.151 88.944 3818 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % 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: 0.55 (0.24), residues: 1236 helix: 0.74 (0.18), residues: 833 sheet: -0.80 (0.86), residues: 42 loop : -0.11 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.014 0.001 TYR A 468 PHE 0.013 0.001 PHE A 550 TRP 0.007 0.001 TRP C 209 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00846 (10202) covalent geometry : angle 1.09220 (13837) hydrogen bonds : bond 0.15084 ( 595) hydrogen bonds : angle 6.08278 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8962 (tt) cc_final: 0.8419 (tt) REVERT: A 587 VAL cc_start: 0.9396 (t) cc_final: 0.9103 (m) REVERT: C 111 ILE cc_start: 0.9279 (tt) cc_final: 0.9074 (tp) REVERT: C 122 GLN cc_start: 0.8766 (tt0) cc_final: 0.8501 (mt0) REVERT: C 160 ASP cc_start: 0.8031 (t0) cc_final: 0.7821 (m-30) REVERT: C 191 HIS cc_start: 0.8450 (m90) cc_final: 0.8067 (m90) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0972 time to fit residues: 20.8581 Evaluate side-chains 91 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN B 82 HIS B 205 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS B 330 GLN C 61 GLN C 241 HIS C 272 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056786 restraints weight = 35823.274| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.85 r_work: 0.3040 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10202 Z= 0.145 Angle : 0.578 8.604 13837 Z= 0.291 Chirality : 0.040 0.125 1575 Planarity : 0.004 0.038 1778 Dihedral : 4.359 71.003 1344 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.17 % Allowed : 17.16 % Favored : 81.66 % 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: 1.37 (0.24), residues: 1236 helix: 1.43 (0.18), residues: 841 sheet: -1.16 (0.73), residues: 47 loop : 0.11 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.014 0.001 TYR C 91 PHE 0.023 0.001 PHE A 550 TRP 0.007 0.001 TRP C 209 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00331 (10202) covalent geometry : angle 0.57835 (13837) hydrogen bonds : bond 0.03624 ( 595) hydrogen bonds : angle 4.56665 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.9135 (tpp) cc_final: 0.8923 (mmp) REVERT: B 356 MET cc_start: 0.9086 (mmt) cc_final: 0.8849 (mmt) REVERT: C 122 GLN cc_start: 0.9003 (tt0) cc_final: 0.8699 (mt0) REVERT: C 191 HIS cc_start: 0.8770 (m90) cc_final: 0.8286 (m90) outliers start: 13 outliers final: 7 residues processed: 109 average time/residue: 0.0809 time to fit residues: 13.4177 Evaluate side-chains 92 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** 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 = 0.3502 r_free = 0.3502 target = 0.069857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057397 restraints weight = 35761.156| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.85 r_work: 0.3051 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10202 Z= 0.112 Angle : 0.544 11.154 13837 Z= 0.270 Chirality : 0.039 0.120 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.225 64.324 1344 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 18.07 % Favored : 80.13 % 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: 1.61 (0.25), residues: 1236 helix: 1.64 (0.18), residues: 849 sheet: -1.22 (0.73), residues: 47 loop : 0.09 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.012 0.001 TYR C 91 PHE 0.021 0.001 PHE A 550 TRP 0.006 0.001 TRP A 489 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00256 (10202) covalent geometry : angle 0.54378 (13837) hydrogen bonds : bond 0.03105 ( 595) hydrogen bonds : angle 4.28912 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7862 (p0) REVERT: A 400 LEU cc_start: 0.9416 (tp) cc_final: 0.9180 (tp) REVERT: A 586 ASP cc_start: 0.8472 (m-30) cc_final: 0.8176 (m-30) REVERT: B 94 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8787 (mm-30) REVERT: B 169 GLU cc_start: 0.9233 (tp30) cc_final: 0.9021 (tp30) REVERT: C 50 CYS cc_start: 0.8817 (m) cc_final: 0.8607 (m) REVERT: C 122 GLN cc_start: 0.9024 (tt0) cc_final: 0.8690 (mt0) REVERT: C 191 HIS cc_start: 0.8835 (m90) cc_final: 0.8236 (m90) outliers start: 20 outliers final: 10 residues processed: 111 average time/residue: 0.0973 time to fit residues: 15.8366 Evaluate side-chains 97 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** 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 = 0.3496 r_free = 0.3496 target = 0.069612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057126 restraints weight = 35946.230| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.86 r_work: 0.3045 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10202 Z= 0.115 Angle : 0.537 10.006 13837 Z= 0.263 Chirality : 0.038 0.126 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.116 57.090 1344 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 17.34 % Favored : 80.85 % 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: 1.76 (0.25), residues: 1236 helix: 1.77 (0.18), residues: 850 sheet: -1.16 (0.75), residues: 47 loop : 0.10 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.015 0.001 TYR C 91 PHE 0.015 0.001 PHE A 550 TRP 0.006 0.001 TRP C 143 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00265 (10202) covalent geometry : angle 0.53655 (13837) hydrogen bonds : bond 0.02898 ( 595) hydrogen bonds : angle 4.16504 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 118 ASP cc_start: 0.8790 (m-30) cc_final: 0.8487 (m-30) REVERT: A 362 MET cc_start: 0.8283 (mmt) cc_final: 0.7415 (mmt) REVERT: A 400 LEU cc_start: 0.9479 (tp) cc_final: 0.9170 (tp) REVERT: A 586 ASP cc_start: 0.8494 (m-30) cc_final: 0.8202 (m-30) REVERT: B 70 ARG cc_start: 0.9570 (ttp-170) cc_final: 0.9241 (ttp80) REVERT: B 169 GLU cc_start: 0.9255 (tp30) cc_final: 0.8945 (tp30) REVERT: B 324 MET cc_start: 0.9021 (mtm) cc_final: 0.8624 (mtm) REVERT: B 356 MET cc_start: 0.9132 (mmt) cc_final: 0.8871 (mmt) REVERT: C 50 CYS cc_start: 0.8941 (m) cc_final: 0.8728 (m) REVERT: C 122 GLN cc_start: 0.9015 (tt0) cc_final: 0.8675 (mt0) REVERT: C 191 HIS cc_start: 0.8812 (m90) cc_final: 0.8217 (m90) REVERT: C 246 GLU cc_start: 0.8956 (tp30) cc_final: 0.8741 (pt0) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.1002 time to fit residues: 15.8800 Evaluate side-chains 96 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.069213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056935 restraints weight = 35588.970| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.79 r_work: 0.3038 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10202 Z= 0.120 Angle : 0.543 9.807 13837 Z= 0.264 Chirality : 0.038 0.166 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.046 51.891 1344 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.53 % Allowed : 17.89 % Favored : 79.58 % 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: 1.80 (0.25), residues: 1236 helix: 1.79 (0.18), residues: 852 sheet: -1.24 (0.75), residues: 47 loop : 0.17 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 239 TYR 0.015 0.001 TYR C 91 PHE 0.012 0.001 PHE A 550 TRP 0.007 0.001 TRP C 143 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00281 (10202) covalent geometry : angle 0.54320 (13837) hydrogen bonds : bond 0.02918 ( 595) hydrogen bonds : angle 4.13567 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 362 MET cc_start: 0.8341 (mmt) cc_final: 0.7383 (mmt) REVERT: A 400 LEU cc_start: 0.9496 (tp) cc_final: 0.9153 (tp) REVERT: A 586 ASP cc_start: 0.8557 (m-30) cc_final: 0.8254 (m-30) REVERT: B 47 ARG cc_start: 0.9265 (mpp80) cc_final: 0.9014 (mpp80) REVERT: B 70 ARG cc_start: 0.9547 (ttp-170) cc_final: 0.9184 (ttp80) REVERT: B 169 GLU cc_start: 0.9272 (tp30) cc_final: 0.8935 (tp30) REVERT: B 324 MET cc_start: 0.9129 (mtm) cc_final: 0.8577 (mpp) REVERT: C 50 CYS cc_start: 0.8950 (m) cc_final: 0.8732 (m) REVERT: C 122 GLN cc_start: 0.9023 (tt0) cc_final: 0.8660 (mt0) REVERT: C 191 HIS cc_start: 0.8793 (m90) cc_final: 0.8170 (m90) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.1059 time to fit residues: 17.4280 Evaluate side-chains 105 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 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 = 0.3498 r_free = 0.3498 target = 0.069712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057225 restraints weight = 36037.520| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.87 r_work: 0.3046 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10202 Z= 0.109 Angle : 0.555 9.976 13837 Z= 0.266 Chirality : 0.038 0.147 1575 Planarity : 0.004 0.040 1778 Dihedral : 3.994 47.280 1344 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.08 % Allowed : 18.43 % Favored : 79.49 % 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: 1.88 (0.25), residues: 1236 helix: 1.84 (0.18), residues: 853 sheet: -1.13 (0.77), residues: 47 loop : 0.21 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.012 0.001 TYR C 91 PHE 0.020 0.001 PHE B 235 TRP 0.007 0.001 TRP C 143 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00254 (10202) covalent geometry : angle 0.55461 (13837) hydrogen bonds : bond 0.02784 ( 595) hydrogen bonds : angle 4.08959 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 118 ASP cc_start: 0.8782 (m-30) cc_final: 0.8473 (m-30) REVERT: A 362 MET cc_start: 0.8301 (mmt) cc_final: 0.7464 (mmt) REVERT: A 400 LEU cc_start: 0.9502 (tp) cc_final: 0.9141 (tp) REVERT: A 586 ASP cc_start: 0.8574 (m-30) cc_final: 0.8266 (m-30) REVERT: B 70 ARG cc_start: 0.9554 (ttp-170) cc_final: 0.9231 (ttp80) REVERT: B 169 GLU cc_start: 0.9270 (tp30) cc_final: 0.8923 (tp30) REVERT: C 50 CYS cc_start: 0.8910 (m) cc_final: 0.8566 (m) REVERT: C 122 GLN cc_start: 0.8996 (tt0) cc_final: 0.8625 (mt0) REVERT: C 160 ASP cc_start: 0.8337 (m-30) cc_final: 0.7839 (m-30) REVERT: C 191 HIS cc_start: 0.8798 (m90) cc_final: 0.8161 (m90) outliers start: 23 outliers final: 17 residues processed: 108 average time/residue: 0.1079 time to fit residues: 16.6018 Evaluate side-chains 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 131 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.067463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054865 restraints weight = 36477.155| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.84 r_work: 0.2987 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10202 Z= 0.180 Angle : 0.597 9.822 13837 Z= 0.289 Chirality : 0.040 0.158 1575 Planarity : 0.004 0.039 1778 Dihedral : 4.081 43.495 1344 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.26 % Allowed : 19.24 % Favored : 78.50 % 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: 1.72 (0.25), residues: 1236 helix: 1.79 (0.18), residues: 853 sheet: -1.46 (0.75), residues: 47 loop : -0.02 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.016 0.001 TYR C 91 PHE 0.017 0.001 PHE B 235 TRP 0.012 0.001 TRP A 269 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00422 (10202) covalent geometry : angle 0.59748 (13837) hydrogen bonds : bond 0.03294 ( 595) hydrogen bonds : angle 4.23248 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8922 (mmm) REVERT: A 362 MET cc_start: 0.8379 (mmt) cc_final: 0.7511 (mmt) REVERT: A 503 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8640 (t0) REVERT: B 70 ARG cc_start: 0.9548 (ttp-170) cc_final: 0.9200 (ttp80) REVERT: B 94 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8876 (mm-30) REVERT: B 169 GLU cc_start: 0.9285 (tp30) cc_final: 0.8897 (tp30) REVERT: C 50 CYS cc_start: 0.9018 (m) cc_final: 0.8718 (m) REVERT: C 160 ASP cc_start: 0.8399 (m-30) cc_final: 0.7932 (m-30) outliers start: 25 outliers final: 18 residues processed: 108 average time/residue: 0.1026 time to fit residues: 15.9812 Evaluate side-chains 102 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.067545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054995 restraints weight = 36395.980| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.82 r_work: 0.2992 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10202 Z= 0.164 Angle : 0.605 8.753 13837 Z= 0.291 Chirality : 0.040 0.176 1575 Planarity : 0.004 0.039 1778 Dihedral : 4.108 42.478 1344 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 19.69 % Favored : 77.87 % 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: 1.67 (0.25), residues: 1236 helix: 1.72 (0.18), residues: 851 sheet: -1.57 (0.74), residues: 47 loop : 0.08 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.014 0.001 TYR B 138 PHE 0.016 0.001 PHE B 235 TRP 0.031 0.001 TRP A 269 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00388 (10202) covalent geometry : angle 0.60465 (13837) hydrogen bonds : bond 0.03194 ( 595) hydrogen bonds : angle 4.22091 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8992 (mmm) REVERT: A 362 MET cc_start: 0.8407 (mmt) cc_final: 0.7484 (mmt) REVERT: A 503 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8658 (t0) REVERT: B 70 ARG cc_start: 0.9561 (ttp-170) cc_final: 0.9200 (ttp80) REVERT: B 103 MET cc_start: 0.8917 (tpp) cc_final: 0.8651 (tpp) REVERT: B 169 GLU cc_start: 0.9295 (tp30) cc_final: 0.8913 (tp30) REVERT: C 50 CYS cc_start: 0.9028 (m) cc_final: 0.8705 (m) REVERT: C 160 ASP cc_start: 0.8396 (m-30) cc_final: 0.7919 (m-30) outliers start: 27 outliers final: 20 residues processed: 106 average time/residue: 0.1000 time to fit residues: 15.3364 Evaluate side-chains 107 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** 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 = 0.3467 r_free = 0.3467 target = 0.068188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055685 restraints weight = 35947.515| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.85 r_work: 0.3007 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10202 Z= 0.133 Angle : 0.593 10.150 13837 Z= 0.283 Chirality : 0.040 0.151 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.069 40.827 1344 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.08 % Allowed : 20.33 % Favored : 77.60 % 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: 1.72 (0.25), residues: 1236 helix: 1.75 (0.18), residues: 851 sheet: -1.52 (0.74), residues: 47 loop : 0.13 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.015 0.001 TYR B 138 PHE 0.013 0.001 PHE B 235 TRP 0.032 0.001 TRP A 269 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (10202) covalent geometry : angle 0.59269 (13837) hydrogen bonds : bond 0.03053 ( 595) hydrogen bonds : angle 4.18472 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9046 (mmm) REVERT: A 362 MET cc_start: 0.8387 (mmt) cc_final: 0.7454 (mmt) REVERT: A 503 ASN cc_start: 0.9033 (m-40) cc_final: 0.8641 (t0) REVERT: B 70 ARG cc_start: 0.9576 (ttp-170) cc_final: 0.9197 (ttp80) REVERT: B 103 MET cc_start: 0.8824 (tpp) cc_final: 0.8521 (tpp) REVERT: B 169 GLU cc_start: 0.9277 (tp30) cc_final: 0.8904 (tp30) REVERT: C 50 CYS cc_start: 0.9001 (m) cc_final: 0.8625 (m) REVERT: C 160 ASP cc_start: 0.8356 (m-30) cc_final: 0.7852 (m-30) outliers start: 23 outliers final: 19 residues processed: 104 average time/residue: 0.0983 time to fit residues: 14.7470 Evaluate side-chains 105 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.068627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056133 restraints weight = 35711.037| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.81 r_work: 0.3024 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10202 Z= 0.124 Angle : 0.599 9.903 13837 Z= 0.286 Chirality : 0.040 0.316 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.041 39.648 1344 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 20.51 % Favored : 77.60 % 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: 1.74 (0.25), residues: 1236 helix: 1.75 (0.18), residues: 851 sheet: -1.46 (0.74), residues: 47 loop : 0.16 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.015 0.001 TYR C 91 PHE 0.012 0.001 PHE B 235 TRP 0.033 0.001 TRP A 269 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00291 (10202) covalent geometry : angle 0.59879 (13837) hydrogen bonds : bond 0.02981 ( 595) hydrogen bonds : angle 4.20461 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9039 (mmm) REVERT: A 362 MET cc_start: 0.8354 (mmt) cc_final: 0.7493 (mmt) REVERT: A 503 ASN cc_start: 0.9020 (m-40) cc_final: 0.8624 (t0) REVERT: B 70 ARG cc_start: 0.9545 (ttp-170) cc_final: 0.9231 (ttp80) REVERT: B 94 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8816 (mm-30) REVERT: B 103 MET cc_start: 0.8857 (tpp) cc_final: 0.8624 (tpp) REVERT: B 169 GLU cc_start: 0.9272 (tp30) cc_final: 0.8908 (tp30) REVERT: B 324 MET cc_start: 0.9038 (mtp) cc_final: 0.8793 (mpp) REVERT: C 50 CYS cc_start: 0.8974 (m) cc_final: 0.8597 (m) REVERT: C 160 ASP cc_start: 0.8294 (m-30) cc_final: 0.7797 (m-30) outliers start: 21 outliers final: 20 residues processed: 106 average time/residue: 0.1032 time to fit residues: 15.8014 Evaluate side-chains 103 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.0020 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 121 optimal weight: 0.0370 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.069773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057233 restraints weight = 35646.674| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.83 r_work: 0.3052 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10202 Z= 0.109 Angle : 0.612 11.192 13837 Z= 0.291 Chirality : 0.040 0.254 1575 Planarity : 0.004 0.041 1778 Dihedral : 4.031 38.484 1344 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.63 % Allowed : 21.41 % Favored : 76.96 % 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: 1.73 (0.25), residues: 1236 helix: 1.73 (0.18), residues: 852 sheet: -1.31 (0.75), residues: 47 loop : 0.16 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 47 TYR 0.014 0.001 TYR B 138 PHE 0.011 0.001 PHE A 550 TRP 0.035 0.001 TRP A 269 HIS 0.003 0.000 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00243 (10202) covalent geometry : angle 0.61218 (13837) hydrogen bonds : bond 0.02855 ( 595) hydrogen bonds : angle 4.19662 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.86 seconds wall clock time: 38 minutes 5.37 seconds (2285.37 seconds total)