Starting phenix.real_space_refine on Mon Jul 28 05:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mf5_48224/07_2025/9mf5_48224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mf5_48224/07_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_48224/07_2025/9mf5_48224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mf5_48224/07_2025/9mf5_48224.map" model { file = "/net/cci-nas-00/data/ceres_data/9mf5_48224/07_2025/9mf5_48224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mf5_48224/07_2025/9mf5_48224.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.57 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 2.92 Time building geometry restraints manager: 3.13 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: 0.700 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (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 TRP 0.007 0.001 TRP C 209 HIS 0.004 0.001 HIS C 241 PHE 0.013 0.001 PHE A 550 TYR 0.014 0.001 TYR A 468 ARG 0.004 0.001 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.15084 ( 595) hydrogen bonds : angle 6.08278 ( 1749) covalent geometry : bond 0.00846 (10202) covalent geometry : angle 1.09220 (13837) *********************** 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 : 1.134 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: 0.8500 (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: 0.2386 time to fit residues: 50.7300 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 : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 61 GLN C 241 HIS C 272 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057706 restraints weight = 35361.596| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.84 r_work: 0.3063 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10202 Z= 0.124 Angle : 0.571 8.755 13837 Z= 0.287 Chirality : 0.039 0.128 1575 Planarity : 0.004 0.037 1778 Dihedral : 4.338 71.165 1344 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.17 % Allowed : 17.07 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1236 helix: 1.44 (0.18), residues: 842 sheet: -1.11 (0.73), residues: 47 loop : 0.16 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 250 HIS 0.005 0.001 HIS C 191 PHE 0.022 0.001 PHE A 550 TYR 0.013 0.001 TYR C 91 ARG 0.004 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 595) hydrogen bonds : angle 4.54097 ( 1749) covalent geometry : bond 0.00278 (10202) covalent geometry : angle 0.57110 (13837) *********************** 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 120 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 TYR cc_start: 0.8342 (p90) cc_final: 0.8128 (p90) REVERT: B 356 MET cc_start: 0.9059 (mmt) cc_final: 0.8838 (mmt) REVERT: C 122 GLN cc_start: 0.8983 (tt0) cc_final: 0.8682 (mt0) REVERT: C 191 HIS cc_start: 0.8770 (m90) cc_final: 0.8266 (m90) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 0.1943 time to fit residues: 33.8511 Evaluate side-chains 90 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain C residue 257 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 131 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057193 restraints weight = 35684.684| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.87 r_work: 0.3045 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1871 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= 0.121 Angle : 0.549 10.942 13837 Z= 0.272 Chirality : 0.039 0.122 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.198 63.939 1344 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 17.25 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1236 helix: 1.63 (0.18), residues: 850 sheet: -1.18 (0.74), residues: 47 loop : 0.14 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 489 HIS 0.004 0.001 HIS C 167 PHE 0.021 0.001 PHE A 550 TYR 0.012 0.001 TYR C 91 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 595) hydrogen bonds : angle 4.29492 ( 1749) covalent geometry : bond 0.00277 (10202) covalent geometry : angle 0.54933 (13837) *********************** 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 116 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.8273 (mmt) cc_final: 0.7401 (mmt) REVERT: B 94 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8794 (mm-30) REVERT: B 169 GLU cc_start: 0.9231 (tp30) cc_final: 0.9015 (tp30) REVERT: C 50 CYS cc_start: 0.8850 (m) cc_final: 0.8581 (m) REVERT: C 122 GLN cc_start: 0.9016 (tt0) cc_final: 0.8688 (mt0) REVERT: C 160 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: C 191 HIS cc_start: 0.8841 (m90) cc_final: 0.8260 (m90) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 0.2058 time to fit residues: 32.7799 Evaluate side-chains 99 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 342 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.057104 restraints weight = 35679.572| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.83 r_work: 0.3045 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 0.037 10202 Z= 0.118 Angle : 0.541 10.309 13837 Z= 0.264 Chirality : 0.038 0.126 1575 Planarity : 0.004 0.041 1778 Dihedral : 4.125 57.085 1344 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.81 % Allowed : 17.80 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1236 helix: 1.74 (0.18), residues: 851 sheet: -1.18 (0.75), residues: 47 loop : 0.16 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 489 HIS 0.003 0.001 HIS C 167 PHE 0.015 0.001 PHE A 550 TYR 0.016 0.001 TYR C 91 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 595) hydrogen bonds : angle 4.17045 ( 1749) covalent geometry : bond 0.00275 (10202) covalent geometry : angle 0.54084 (13837) *********************** 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 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8787 (m-30) cc_final: 0.8481 (m-30) REVERT: A 362 MET cc_start: 0.8303 (mmt) cc_final: 0.7426 (mmt) REVERT: B 70 ARG cc_start: 0.9555 (ttp-170) cc_final: 0.9238 (ttp80) REVERT: B 169 GLU cc_start: 0.9255 (tp30) cc_final: 0.8943 (tp30) REVERT: B 324 MET cc_start: 0.9041 (ptt) cc_final: 0.8840 (ptp) REVERT: B 356 MET cc_start: 0.9140 (mmt) cc_final: 0.8897 (mmt) REVERT: C 50 CYS cc_start: 0.8949 (m) cc_final: 0.8731 (m) REVERT: C 122 GLN cc_start: 0.9003 (tt0) cc_final: 0.8672 (mt0) REVERT: C 191 HIS cc_start: 0.8815 (m90) cc_final: 0.8246 (m90) REVERT: C 246 GLU cc_start: 0.8948 (tp30) cc_final: 0.8738 (pt0) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.2262 time to fit residues: 34.6883 Evaluate side-chains 94 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057392 restraints weight = 35461.324| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.84 r_work: 0.3051 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10202 Z= 0.105 Angle : 0.532 10.226 13837 Z= 0.258 Chirality : 0.038 0.125 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.049 53.011 1344 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 18.43 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1236 helix: 1.78 (0.18), residues: 852 sheet: -1.12 (0.76), residues: 47 loop : 0.16 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 143 HIS 0.003 0.000 HIS C 167 PHE 0.013 0.001 PHE A 550 TYR 0.015 0.001 TYR C 91 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 595) hydrogen bonds : angle 4.11350 ( 1749) covalent geometry : bond 0.00243 (10202) covalent geometry : angle 0.53221 (13837) *********************** 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 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.8318 (mmt) cc_final: 0.7434 (mmt) REVERT: B 47 ARG cc_start: 0.9269 (mpp80) cc_final: 0.9020 (mpp80) REVERT: B 70 ARG cc_start: 0.9562 (ttp-170) cc_final: 0.9239 (ttp80) REVERT: B 169 GLU cc_start: 0.9275 (tp30) cc_final: 0.8945 (tp30) REVERT: C 50 CYS cc_start: 0.8938 (m) cc_final: 0.8716 (m) REVERT: C 122 GLN cc_start: 0.8973 (tt0) cc_final: 0.8633 (mt0) REVERT: C 191 HIS cc_start: 0.8762 (m90) cc_final: 0.8154 (m90) REVERT: C 246 GLU cc_start: 0.8955 (tp30) cc_final: 0.8753 (pt0) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.2147 time to fit residues: 32.2784 Evaluate side-chains 98 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 23 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 283 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.066115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053614 restraints weight = 36631.221| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.77 r_work: 0.2954 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10202 Z= 0.246 Angle : 0.626 9.249 13837 Z= 0.309 Chirality : 0.041 0.122 1575 Planarity : 0.004 0.039 1778 Dihedral : 4.228 48.022 1344 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 17.71 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1236 helix: 1.66 (0.18), residues: 846 sheet: -1.37 (0.78), residues: 43 loop : -0.08 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 209 HIS 0.007 0.001 HIS C 167 PHE 0.020 0.002 PHE B 235 TYR 0.021 0.001 TYR C 91 ARG 0.004 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 595) hydrogen bonds : angle 4.35350 ( 1749) covalent geometry : bond 0.00570 (10202) covalent geometry : angle 0.62587 (13837) *********************** 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 111 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8826 (mt) REVERT: A 362 MET cc_start: 0.8527 (mmt) cc_final: 0.7563 (mmt) REVERT: A 503 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8687 (t0) REVERT: B 70 ARG cc_start: 0.9545 (ttp-170) cc_final: 0.9117 (ttp80) REVERT: C 50 CYS cc_start: 0.9074 (m) cc_final: 0.8771 (m) REVERT: C 160 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7856 (m-30) outliers start: 32 outliers final: 22 residues processed: 101 average time/residue: 0.2147 time to fit residues: 31.4235 Evaluate side-chains 101 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 251 ASP 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 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 334 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 166 LEU 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 79 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.068392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055883 restraints weight = 36458.250| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.85 r_work: 0.3014 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10202 Z= 0.118 Angle : 0.573 9.566 13837 Z= 0.275 Chirality : 0.039 0.151 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.116 45.635 1344 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.08 % Allowed : 18.79 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1236 helix: 1.73 (0.18), residues: 852 sheet: -1.34 (0.75), residues: 47 loop : 0.04 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 143 HIS 0.004 0.001 HIS C 167 PHE 0.016 0.001 PHE B 235 TYR 0.016 0.001 TYR A 273 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 595) hydrogen bonds : angle 4.14237 ( 1749) covalent geometry : bond 0.00278 (10202) covalent geometry : angle 0.57264 (13837) *********************** 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 114 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.8377 (mmt) cc_final: 0.7435 (mmt) REVERT: A 503 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8653 (t0) REVERT: B 70 ARG cc_start: 0.9572 (ttp-170) cc_final: 0.9191 (ttp80) REVERT: B 94 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8890 (mm-30) REVERT: B 103 MET cc_start: 0.8860 (tpp) cc_final: 0.8438 (tpp) REVERT: B 156 LYS cc_start: 0.9554 (pttt) cc_final: 0.9183 (ttmt) REVERT: B 169 GLU cc_start: 0.9260 (tp30) cc_final: 0.8990 (tp30) REVERT: B 356 MET cc_start: 0.9099 (mmt) cc_final: 0.8881 (mmt) REVERT: C 50 CYS cc_start: 0.8978 (m) cc_final: 0.8603 (m) REVERT: C 160 ASP cc_start: 0.8335 (m-30) cc_final: 0.7794 (m-30) outliers start: 23 outliers final: 17 residues processed: 106 average time/residue: 0.2157 time to fit residues: 32.8056 Evaluate side-chains 104 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 306 CYS 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 75 SER Chi-restraints excluded: chain C residue 165 CYS 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 39 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.068355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055797 restraints weight = 36306.594| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.85 r_work: 0.3012 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2547 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= 0.128 Angle : 0.582 9.828 13837 Z= 0.278 Chirality : 0.039 0.140 1575 Planarity : 0.004 0.040 1778 Dihedral : 4.061 42.476 1344 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.90 % Allowed : 19.42 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1236 helix: 1.77 (0.18), residues: 851 sheet: -1.36 (0.74), residues: 47 loop : 0.05 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 143 HIS 0.004 0.001 HIS C 167 PHE 0.015 0.001 PHE B 235 TYR 0.016 0.001 TYR C 91 ARG 0.003 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 595) hydrogen bonds : angle 4.14702 ( 1749) covalent geometry : bond 0.00300 (10202) covalent geometry : angle 0.58188 (13837) *********************** 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 110 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9294 (mp) cc_final: 0.9014 (mt) REVERT: A 118 ASP cc_start: 0.9190 (m-30) cc_final: 0.8887 (m-30) REVERT: A 362 MET cc_start: 0.8380 (mmt) cc_final: 0.7444 (mmt) REVERT: B 70 ARG cc_start: 0.9582 (ttp-170) cc_final: 0.9205 (ttp80) REVERT: B 103 MET cc_start: 0.8820 (tpp) cc_final: 0.8575 (tpp) REVERT: B 156 LYS cc_start: 0.9556 (pttt) cc_final: 0.9194 (ttmt) REVERT: B 169 GLU cc_start: 0.9276 (tp30) cc_final: 0.8977 (tp30) REVERT: B 356 MET cc_start: 0.9109 (mmt) cc_final: 0.8870 (mmt) REVERT: C 50 CYS cc_start: 0.8990 (m) cc_final: 0.8625 (m) REVERT: C 160 ASP cc_start: 0.8380 (m-30) cc_final: 0.7874 (m-30) outliers start: 21 outliers final: 19 residues processed: 104 average time/residue: 0.2252 time to fit residues: 34.2693 Evaluate side-chains 107 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 306 CYS 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 230 SER 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 75 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 165 CYS 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 81 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** C 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.069509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057077 restraints weight = 35746.919| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.83 r_work: 0.3049 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10202 Z= 0.106 Angle : 0.584 8.907 13837 Z= 0.277 Chirality : 0.038 0.157 1575 Planarity : 0.004 0.041 1778 Dihedral : 4.003 39.912 1344 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.54 % Allowed : 20.23 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1236 helix: 1.81 (0.18), residues: 851 sheet: -1.27 (0.75), residues: 47 loop : 0.13 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 143 HIS 0.003 0.000 HIS A 99 PHE 0.011 0.001 PHE B 235 TYR 0.014 0.001 TYR C 91 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 595) hydrogen bonds : angle 4.09486 ( 1749) covalent geometry : bond 0.00241 (10202) covalent geometry : angle 0.58422 (13837) *********************** 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 112 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9256 (mp) cc_final: 0.8941 (mt) REVERT: A 118 ASP cc_start: 0.9160 (m-30) cc_final: 0.8856 (m-30) REVERT: B 103 MET cc_start: 0.8834 (tpp) cc_final: 0.8509 (tpp) REVERT: B 156 LYS cc_start: 0.9548 (pttt) cc_final: 0.9206 (tttp) REVERT: B 169 GLU cc_start: 0.9269 (tp30) cc_final: 0.8965 (tp30) REVERT: B 303 MET cc_start: 0.8768 (mtm) cc_final: 0.8551 (ttm) REVERT: B 356 MET cc_start: 0.9115 (mmt) cc_final: 0.8847 (mmt) REVERT: C 50 CYS cc_start: 0.8947 (m) cc_final: 0.8573 (m) REVERT: C 83 MET cc_start: 0.7120 (mtt) cc_final: 0.6827 (mtt) REVERT: C 160 ASP cc_start: 0.8283 (m-30) cc_final: 0.7781 (m-30) outliers start: 17 outliers final: 15 residues processed: 108 average time/residue: 0.2386 time to fit residues: 37.5151 Evaluate side-chains 103 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 306 CYS Chi-restraints excluded: chain A residue 416 LEU 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 387 HIS Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 75 SER 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 89 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.069708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057215 restraints weight = 35934.065| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.85 r_work: 0.3051 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2760 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= 0.111 Angle : 0.597 8.888 13837 Z= 0.289 Chirality : 0.039 0.201 1575 Planarity : 0.004 0.041 1778 Dihedral : 4.011 38.668 1344 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.17 % Allowed : 21.77 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1236 helix: 1.80 (0.18), residues: 851 sheet: -1.30 (0.76), residues: 47 loop : 0.14 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 269 HIS 0.003 0.000 HIS A 99 PHE 0.011 0.001 PHE B 235 TYR 0.048 0.001 TYR A 438 ARG 0.005 0.000 ARG B 376 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 595) hydrogen bonds : angle 4.13701 ( 1749) covalent geometry : bond 0.00255 (10202) covalent geometry : angle 0.59729 (13837) ********************** 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 106 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9244 (mp) cc_final: 0.8930 (mt) REVERT: A 118 ASP cc_start: 0.9154 (m-30) cc_final: 0.8851 (m-30) REVERT: A 362 MET cc_start: 0.8434 (mmt) cc_final: 0.7636 (mmt) REVERT: B 103 MET cc_start: 0.8854 (tpp) cc_final: 0.8510 (tpp) REVERT: B 156 LYS cc_start: 0.9547 (pttt) cc_final: 0.9203 (tttp) REVERT: B 169 GLU cc_start: 0.9277 (tp30) cc_final: 0.8972 (tp30) REVERT: B 356 MET cc_start: 0.9128 (mmt) cc_final: 0.8867 (mmt) REVERT: C 50 CYS cc_start: 0.8930 (m) cc_final: 0.8546 (m) REVERT: C 83 MET cc_start: 0.7275 (mtt) cc_final: 0.6982 (mtt) REVERT: C 160 ASP cc_start: 0.8244 (m-30) cc_final: 0.7726 (m-30) outliers start: 13 outliers final: 12 residues processed: 103 average time/residue: 0.2173 time to fit residues: 32.4280 Evaluate side-chains 103 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 306 CYS 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 397 PHE Chi-restraints excluded: chain C residue 75 SER 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 69 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.069695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057166 restraints weight = 35566.234| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.86 r_work: 0.3049 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10202 Z= 0.114 Angle : 0.605 9.576 13837 Z= 0.292 Chirality : 0.040 0.291 1575 Planarity : 0.004 0.041 1778 Dihedral : 4.020 38.068 1344 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 21.86 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1236 helix: 1.78 (0.18), residues: 851 sheet: -1.37 (0.76), residues: 47 loop : 0.15 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 269 HIS 0.003 0.001 HIS A 99 PHE 0.010 0.001 PHE B 235 TYR 0.044 0.001 TYR A 438 ARG 0.005 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 595) hydrogen bonds : angle 4.15446 ( 1749) covalent geometry : bond 0.00267 (10202) covalent geometry : angle 0.60498 (13837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.52 seconds wall clock time: 74 minutes 41.46 seconds (4481.46 seconds total)