Starting phenix.real_space_refine on Mon Jul 28 13:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.map" model { file = "/net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rag_4774/07_2025/6rag_4774.cif" } resolution = 4.2 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= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6568 2.51 5 N 1797 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4541 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 556} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.17, per 1000 atoms: 0.80 Number of scatterers: 10188 At special positions: 0 Unit cell: (102.315, 92.622, 155.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 2 11.99 O 1791 8.00 N 1797 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 65.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.261A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.178A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 5.012A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 119 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.610A pdb=" N ARG A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 173 removed outlier: 4.341A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 138 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.461A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 222 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 231 through 258 removed outlier: 3.742A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.657A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.771A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 332 removed outlier: 3.645A pdb=" N GLY A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.771A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.861A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.774A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'B' and resid 5 through 18 removed outlier: 4.006A pdb=" N LEU B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 54 Proline residue: B 42 - end of helix removed outlier: 4.006A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 105 removed outlier: 4.111A pdb=" N TYR B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.774A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 133 Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.534A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 207 removed outlier: 3.658A pdb=" N TYR B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.563A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 243 removed outlier: 3.763A pdb=" N ALA B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 271 removed outlier: 4.564A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.631A pdb=" N LEU B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 316 Processing helix chain 'B' and resid 376 through 384 removed outlier: 4.146A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.804A pdb=" N ALA B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.659A pdb=" N VAL B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 462 through 466 removed outlier: 4.270A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.615A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.568A pdb=" N ALA B 535 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 539 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 578 removed outlier: 3.681A pdb=" N GLU B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 379 through 383 removed outlier: 4.979A pdb=" N VAL A 379 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 353 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 5.774A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 389 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 361 removed outlier: 4.474A pdb=" N LEU B 354 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL B 344 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B 358 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 342 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 360 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG B 340 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 341 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR B 396 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY B 343 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 394 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.091A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 496 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 529 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 498 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 367 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 545 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1615 1.31 - 1.44: 2800 1.44 - 1.56: 5924 1.56 - 1.69: 16 1.69 - 1.81: 45 Bond restraints: 10400 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.21e+01 bond pdb=" N PRO A 515 " pdb=" CD PRO A 515 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 1.522 1.593 -0.071 1.39e-02 5.18e+03 2.57e+01 bond pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 13772 3.99 - 7.98: 292 7.98 - 11.96: 44 11.96 - 15.95: 1 15.95 - 19.94: 2 Bond angle restraints: 14111 Sorted by residual: angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.46 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" N VAL B 298 " pdb=" CA VAL B 298 " pdb=" C VAL B 298 " ideal model delta sigma weight residual 110.53 98.04 12.49 9.40e-01 1.13e+00 1.77e+02 angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 112.64 123.80 -11.16 1.21e+00 6.83e-01 8.51e+01 angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 112.97 103.27 9.70 1.06e+00 8.90e-01 8.37e+01 ... (remaining 14106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 5955 29.84 - 59.67: 212 59.67 - 89.51: 22 89.51 - 119.34: 1 119.34 - 149.17: 2 Dihedral angle restraints: 6192 sinusoidal: 2527 harmonic: 3665 Sorted by residual: dihedral pdb=" O1B ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PB ADP A 702 " pdb=" PA ADP A 702 " ideal model delta sinusoidal sigma weight residual 300.00 150.82 149.17 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 62.82 -122.82 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA TRP B 290 " pdb=" C TRP B 290 " pdb=" N PRO B 291 " pdb=" CA PRO B 291 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1335 0.096 - 0.191: 229 0.191 - 0.287: 29 0.287 - 0.383: 9 0.383 - 0.478: 7 Chirality restraints: 1609 Sorted by residual: chirality pdb=" CA ASP B 500 " pdb=" N ASP B 500 " pdb=" C ASP B 500 " pdb=" CB ASP B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA VAL C 102 " pdb=" N VAL C 102 " pdb=" C VAL C 102 " pdb=" CB VAL C 102 " both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 1606 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 138 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR A 138 " -0.082 2.00e-02 2.50e+03 pdb=" O THR A 138 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 139 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 23 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 24 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 243 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO B 244 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " -0.040 5.00e-02 4.00e+02 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 32 2.51 - 3.11: 7067 3.11 - 3.70: 15963 3.70 - 4.30: 21137 4.30 - 4.90: 34422 Nonbonded interactions: 78621 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O1B ATP B 602 " model vdw 1.911 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1G ATP B 602 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 601 " model vdw 2.024 2.170 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 601 " model vdw 2.050 2.170 nonbonded pdb=" O THR A 400 " pdb=" OG SER A 404 " model vdw 2.252 3.040 ... (remaining 78616 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 group one per residue 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: 229.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 265.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 10402 Z= 0.510 Angle : 1.420 19.938 14115 Z= 0.926 Chirality : 0.079 0.478 1609 Planarity : 0.008 0.078 1785 Dihedral : 15.357 149.175 3840 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.67 % Allowed : 12.20 % Favored : 87.13 % Cbeta Deviations : 0.43 % 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: -3.67 (0.18), residues: 1276 helix: -2.48 (0.14), residues: 768 sheet: -0.57 (0.43), residues: 124 loop : -2.52 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 193 HIS 0.012 0.002 HIS B 100 PHE 0.025 0.003 PHE A 147 TYR 0.029 0.003 TYR A 588 ARG 0.011 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.17221 ( 634) hydrogen bonds : angle 6.95447 ( 1863) SS BOND : bond 0.02172 ( 2) SS BOND : angle 2.02293 ( 4) covalent geometry : bond 0.00968 (10400) covalent geometry : angle 1.41955 (14111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 273 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.7289 (m-10) cc_final: 0.7011 (m-80) REVERT: A 118 MET cc_start: 0.9224 (mmt) cc_final: 0.9007 (tpp) REVERT: A 166 LEU cc_start: 0.8440 (tp) cc_final: 0.7972 (tt) REVERT: A 205 MET cc_start: 0.8817 (tmm) cc_final: 0.8548 (tmm) REVERT: A 218 GLU cc_start: 0.8421 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 375 VAL cc_start: 0.0141 (OUTLIER) cc_final: -0.0356 (t) REVERT: A 430 GLU cc_start: 0.8154 (pt0) cc_final: 0.7393 (mt-10) REVERT: A 508 VAL cc_start: 0.8884 (p) cc_final: 0.8679 (m) REVERT: A 560 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8472 (tpp80) REVERT: B 25 LEU cc_start: 0.8800 (tp) cc_final: 0.8360 (tt) REVERT: B 32 LEU cc_start: 0.8447 (mt) cc_final: 0.8210 (mp) REVERT: B 154 MET cc_start: 0.8952 (ttt) cc_final: 0.8295 (ttt) REVERT: B 191 GLN cc_start: 0.8146 (pp30) cc_final: 0.7895 (tm-30) REVERT: B 228 ASN cc_start: 0.9239 (t0) cc_final: 0.8898 (t0) REVERT: B 253 MET cc_start: 0.8825 (mmt) cc_final: 0.8625 (mmp) REVERT: B 347 LYS cc_start: 0.7606 (tptt) cc_final: 0.7003 (tppt) REVERT: B 412 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8478 (mtmm) REVERT: B 436 LEU cc_start: 0.9108 (tp) cc_final: 0.8888 (tp) REVERT: B 521 LEU cc_start: 0.8826 (tp) cc_final: 0.8469 (mp) REVERT: B 558 SER cc_start: 0.9095 (m) cc_final: 0.8819 (t) REVERT: B 559 LEU cc_start: 0.9062 (mt) cc_final: 0.8849 (mt) REVERT: B 569 MET cc_start: 0.6915 (ttm) cc_final: 0.6457 (ttm) REVERT: C 37 PHE cc_start: 0.8313 (m-80) cc_final: 0.8092 (m-80) REVERT: C 53 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8765 (ttmt) REVERT: C 93 VAL cc_start: 0.8760 (m) cc_final: 0.8357 (p) REVERT: C 98 THR cc_start: 0.8955 (m) cc_final: 0.8630 (t) REVERT: C 109 VAL cc_start: 0.8536 (t) cc_final: 0.8227 (t) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.3422 time to fit residues: 128.0494 Evaluate side-chains 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 453 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 111 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 479 GLN B 531 HIS B 556 HIS C 3 GLN C 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088478 restraints weight = 25883.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090803 restraints weight = 16794.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092362 restraints weight = 12458.773| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10402 Z= 0.152 Angle : 0.682 6.637 14115 Z= 0.350 Chirality : 0.043 0.167 1609 Planarity : 0.005 0.062 1785 Dihedral : 7.095 117.513 1483 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.29 % Allowed : 5.53 % Favored : 94.18 % 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 (0.21), residues: 1276 helix: -0.42 (0.17), residues: 777 sheet: -0.71 (0.40), residues: 137 loop : -1.87 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 193 HIS 0.011 0.001 HIS B 111 PHE 0.021 0.001 PHE A 160 TYR 0.025 0.001 TYR A 588 ARG 0.006 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 634) hydrogen bonds : angle 4.90239 ( 1863) SS BOND : bond 0.00765 ( 2) SS BOND : angle 0.70367 ( 4) covalent geometry : bond 0.00329 (10400) covalent geometry : angle 0.68230 (14111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8745 (mm110) cc_final: 0.8475 (mm110) REVERT: A 445 LEU cc_start: 0.8113 (mm) cc_final: 0.7682 (tp) REVERT: A 455 ARG cc_start: 0.8175 (ptt180) cc_final: 0.7866 (ptt-90) REVERT: A 502 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8190 (mtmt) REVERT: B 25 LEU cc_start: 0.8714 (tp) cc_final: 0.8437 (tt) REVERT: B 32 LEU cc_start: 0.8353 (mt) cc_final: 0.8089 (mp) REVERT: B 108 ASP cc_start: 0.7622 (t70) cc_final: 0.6870 (t0) REVERT: B 154 MET cc_start: 0.8751 (ttt) cc_final: 0.8004 (ttt) REVERT: B 253 MET cc_start: 0.8720 (mmt) cc_final: 0.8393 (mmp) REVERT: B 347 LYS cc_start: 0.7342 (tptt) cc_final: 0.6735 (tppt) REVERT: B 365 MET cc_start: 0.7950 (tmm) cc_final: 0.7442 (tmm) REVERT: B 367 LEU cc_start: 0.9631 (tp) cc_final: 0.9335 (tt) REVERT: B 380 LEU cc_start: 0.8766 (tp) cc_final: 0.8542 (tp) REVERT: B 423 LEU cc_start: 0.8885 (mt) cc_final: 0.8523 (pp) REVERT: B 436 LEU cc_start: 0.8886 (tp) cc_final: 0.8678 (tp) REVERT: B 521 LEU cc_start: 0.8684 (tp) cc_final: 0.8216 (mp) REVERT: B 559 LEU cc_start: 0.9308 (mt) cc_final: 0.9101 (mt) REVERT: B 569 MET cc_start: 0.6928 (ttm) cc_final: 0.6370 (ttm) REVERT: B 573 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8196 (tp-100) REVERT: C 3 GLN cc_start: 0.5456 (pt0) cc_final: 0.3901 (pt0) REVERT: C 57 ASN cc_start: 0.7474 (m-40) cc_final: 0.6972 (t0) REVERT: C 65 LYS cc_start: 0.8749 (ptmt) cc_final: 0.8331 (mttt) REVERT: C 93 VAL cc_start: 0.8557 (m) cc_final: 0.8177 (p) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.3264 time to fit residues: 109.6535 Evaluate side-chains 171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 58 optimal weight: 0.0020 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 0.0470 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 531 HIS B 538 HIS C 39 GLN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.116985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088813 restraints weight = 26185.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091170 restraints weight = 16432.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092911 restraints weight = 12050.188| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10402 Z= 0.128 Angle : 0.635 8.391 14115 Z= 0.321 Chirality : 0.042 0.169 1609 Planarity : 0.005 0.056 1785 Dihedral : 6.415 104.352 1483 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % 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: -0.32 (0.23), residues: 1276 helix: 0.56 (0.18), residues: 774 sheet: -0.82 (0.39), residues: 138 loop : -1.46 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 193 HIS 0.004 0.001 HIS C 80 PHE 0.017 0.001 PHE A 478 TYR 0.018 0.001 TYR A 588 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 634) hydrogen bonds : angle 4.45390 ( 1863) SS BOND : bond 0.00427 ( 2) SS BOND : angle 1.32118 ( 4) covalent geometry : bond 0.00266 (10400) covalent geometry : angle 0.63472 (14111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 TRP cc_start: 0.7659 (m100) cc_final: 0.7243 (m100) REVERT: A 376 LEU cc_start: 0.5928 (mt) cc_final: 0.5670 (mt) REVERT: A 444 PHE cc_start: 0.6563 (t80) cc_final: 0.6348 (t80) REVERT: A 445 LEU cc_start: 0.8020 (mm) cc_final: 0.7673 (tt) REVERT: A 502 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8117 (mtmt) REVERT: B 25 LEU cc_start: 0.8668 (tp) cc_final: 0.8420 (tt) REVERT: B 32 LEU cc_start: 0.8198 (mt) cc_final: 0.7687 (mt) REVERT: B 108 ASP cc_start: 0.7619 (t70) cc_final: 0.6864 (t0) REVERT: B 154 MET cc_start: 0.8731 (ttt) cc_final: 0.7862 (ttt) REVERT: B 199 THR cc_start: 0.9055 (m) cc_final: 0.8685 (m) REVERT: B 228 ASN cc_start: 0.9032 (t0) cc_final: 0.8810 (t0) REVERT: B 347 LYS cc_start: 0.7377 (tptt) cc_final: 0.6708 (tppt) REVERT: B 365 MET cc_start: 0.8004 (tmm) cc_final: 0.7598 (tmm) REVERT: B 431 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7702 (t0) REVERT: B 436 LEU cc_start: 0.8832 (tp) cc_final: 0.8616 (tp) REVERT: B 559 LEU cc_start: 0.9390 (mt) cc_final: 0.9169 (mt) REVERT: B 569 MET cc_start: 0.6839 (ttm) cc_final: 0.6259 (ttm) REVERT: C 3 GLN cc_start: 0.6219 (pt0) cc_final: 0.5556 (pt0) REVERT: C 57 ASN cc_start: 0.7197 (m-40) cc_final: 0.6845 (t0) REVERT: C 65 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8530 (mttt) REVERT: C 93 VAL cc_start: 0.8758 (m) cc_final: 0.8370 (p) REVERT: C 94 TYR cc_start: 0.5644 (m-10) cc_final: 0.5111 (m-80) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.2759 time to fit residues: 91.5166 Evaluate side-chains 162 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 120 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 531 HIS C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.117777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090325 restraints weight = 26128.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092720 restraints weight = 16603.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094387 restraints weight = 12134.256| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10402 Z= 0.128 Angle : 0.619 8.190 14115 Z= 0.310 Chirality : 0.041 0.168 1609 Planarity : 0.004 0.052 1785 Dihedral : 5.939 98.411 1483 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 0.25 (0.23), residues: 1276 helix: 1.01 (0.18), residues: 778 sheet: -0.66 (0.38), residues: 145 loop : -1.24 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.002 0.001 HIS A 476 PHE 0.017 0.001 PHE A 160 TYR 0.040 0.001 TYR B 187 ARG 0.004 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 634) hydrogen bonds : angle 4.21979 ( 1863) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.18561 ( 4) covalent geometry : bond 0.00261 (10400) covalent geometry : angle 0.61903 (14111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.8921 (m-80) cc_final: 0.8309 (m-80) REVERT: B 25 LEU cc_start: 0.8586 (tp) cc_final: 0.8375 (tt) REVERT: B 32 LEU cc_start: 0.8148 (mt) cc_final: 0.7630 (mt) REVERT: B 125 ASP cc_start: 0.6871 (m-30) cc_final: 0.6662 (m-30) REVERT: B 154 MET cc_start: 0.8622 (ttt) cc_final: 0.8038 (ttt) REVERT: B 164 TYR cc_start: 0.7654 (m-80) cc_final: 0.7146 (m-80) REVERT: B 199 THR cc_start: 0.9001 (m) cc_final: 0.8603 (m) REVERT: B 347 LYS cc_start: 0.7149 (tptt) cc_final: 0.6619 (tppt) REVERT: B 365 MET cc_start: 0.7975 (tmm) cc_final: 0.7721 (tmm) REVERT: B 436 LEU cc_start: 0.8882 (tp) cc_final: 0.8638 (tp) REVERT: B 521 LEU cc_start: 0.8312 (mt) cc_final: 0.8055 (mp) REVERT: B 559 LEU cc_start: 0.9401 (mt) cc_final: 0.9173 (mt) REVERT: B 569 MET cc_start: 0.6852 (ttm) cc_final: 0.6253 (ttm) REVERT: C 55 THR cc_start: 0.8366 (p) cc_final: 0.8107 (p) REVERT: C 65 LYS cc_start: 0.8926 (ptmt) cc_final: 0.8528 (mttt) REVERT: C 70 ILE cc_start: 0.8449 (tp) cc_final: 0.8170 (mt) REVERT: C 93 VAL cc_start: 0.8741 (m) cc_final: 0.8345 (p) REVERT: C 94 TYR cc_start: 0.5311 (m-10) cc_final: 0.4926 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2431 time to fit residues: 79.4469 Evaluate side-chains 163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 538 HIS ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091333 restraints weight = 26236.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092451 restraints weight = 18462.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093339 restraints weight = 13020.801| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10402 Z= 0.127 Angle : 0.622 8.448 14115 Z= 0.308 Chirality : 0.041 0.194 1609 Planarity : 0.004 0.049 1785 Dihedral : 5.613 93.213 1483 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 0.56 (0.23), residues: 1276 helix: 1.26 (0.19), residues: 766 sheet: -0.55 (0.39), residues: 140 loop : -1.04 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 PHE 0.016 0.001 PHE A 478 TYR 0.030 0.001 TYR B 187 ARG 0.006 0.000 ARG B 443 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 634) hydrogen bonds : angle 4.11970 ( 1863) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.41910 ( 4) covalent geometry : bond 0.00273 (10400) covalent geometry : angle 0.62174 (14111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8890 (pp20) cc_final: 0.8656 (pp20) REVERT: A 299 TYR cc_start: 0.8942 (m-80) cc_final: 0.8331 (m-80) REVERT: A 376 LEU cc_start: 0.6303 (mt) cc_final: 0.6069 (mt) REVERT: A 444 PHE cc_start: 0.6863 (t80) cc_final: 0.6506 (t80) REVERT: B 32 LEU cc_start: 0.8278 (mt) cc_final: 0.7750 (mt) REVERT: B 79 MET cc_start: 0.8955 (tmm) cc_final: 0.8718 (tmm) REVERT: B 125 ASP cc_start: 0.6932 (m-30) cc_final: 0.6712 (m-30) REVERT: B 154 MET cc_start: 0.8558 (ttt) cc_final: 0.7962 (ttt) REVERT: B 199 THR cc_start: 0.9015 (m) cc_final: 0.8618 (m) REVERT: B 253 MET cc_start: 0.8821 (mmp) cc_final: 0.8584 (mmp) REVERT: B 347 LYS cc_start: 0.7538 (tptt) cc_final: 0.6834 (tppt) REVERT: B 365 MET cc_start: 0.8046 (tmm) cc_final: 0.7717 (tmm) REVERT: B 436 LEU cc_start: 0.8870 (tp) cc_final: 0.8616 (tp) REVERT: B 559 LEU cc_start: 0.9419 (mt) cc_final: 0.9137 (mt) REVERT: B 569 MET cc_start: 0.7019 (ttm) cc_final: 0.6310 (ttm) REVERT: C 65 LYS cc_start: 0.8938 (ptmt) cc_final: 0.8538 (mttt) REVERT: C 83 MET cc_start: 0.6566 (mmm) cc_final: 0.5943 (mmp) REVERT: C 93 VAL cc_start: 0.8710 (m) cc_final: 0.8263 (p) REVERT: C 94 TYR cc_start: 0.5465 (m-10) cc_final: 0.4942 (m-80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2241 time to fit residues: 69.1832 Evaluate side-chains 156 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 30 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN B 431 ASN ** B 573 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 = 0.3830 r_free = 0.3830 target = 0.119167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093175 restraints weight = 26207.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095129 restraints weight = 17147.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095841 restraints weight = 11850.649| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10402 Z= 0.117 Angle : 0.623 8.401 14115 Z= 0.304 Chirality : 0.041 0.190 1609 Planarity : 0.004 0.050 1785 Dihedral : 5.119 75.298 1483 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.84 (0.23), residues: 1276 helix: 1.48 (0.18), residues: 778 sheet: -0.52 (0.39), residues: 145 loop : -0.97 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 36 HIS 0.002 0.001 HIS B 454 PHE 0.020 0.001 PHE B 281 TYR 0.024 0.001 TYR B 187 ARG 0.003 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 634) hydrogen bonds : angle 3.95858 ( 1863) SS BOND : bond 0.00789 ( 2) SS BOND : angle 1.18173 ( 4) covalent geometry : bond 0.00238 (10400) covalent geometry : angle 0.62283 (14111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8765 (t0) cc_final: 0.8295 (t70) REVERT: A 205 MET cc_start: 0.8761 (tmm) cc_final: 0.8556 (tmm) REVERT: A 299 TYR cc_start: 0.8907 (m-80) cc_final: 0.8372 (m-80) REVERT: A 376 LEU cc_start: 0.6201 (mt) cc_final: 0.5882 (mt) REVERT: A 444 PHE cc_start: 0.6865 (t80) cc_final: 0.6575 (t80) REVERT: B 32 LEU cc_start: 0.8144 (mt) cc_final: 0.7673 (mt) REVERT: B 79 MET cc_start: 0.8864 (tmm) cc_final: 0.8658 (tmm) REVERT: B 154 MET cc_start: 0.8682 (ttt) cc_final: 0.7835 (ttt) REVERT: B 164 TYR cc_start: 0.7713 (m-80) cc_final: 0.7213 (m-80) REVERT: B 191 GLN cc_start: 0.8604 (mp-120) cc_final: 0.8216 (mp10) REVERT: B 199 THR cc_start: 0.8917 (m) cc_final: 0.8549 (m) REVERT: B 253 MET cc_start: 0.8867 (mmp) cc_final: 0.8603 (mmp) REVERT: B 365 MET cc_start: 0.8039 (tmm) cc_final: 0.7793 (tmm) REVERT: B 380 LEU cc_start: 0.8521 (tp) cc_final: 0.8305 (tp) REVERT: B 436 LEU cc_start: 0.8767 (tp) cc_final: 0.8497 (tp) REVERT: B 499 ASP cc_start: 0.5408 (t0) cc_final: 0.5190 (p0) REVERT: B 528 LEU cc_start: 0.9039 (tp) cc_final: 0.8829 (tt) REVERT: B 559 LEU cc_start: 0.9320 (mt) cc_final: 0.9069 (mt) REVERT: B 569 MET cc_start: 0.6903 (ttm) cc_final: 0.6226 (ttm) REVERT: C 65 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8519 (mttm) REVERT: C 72 ARG cc_start: 0.7707 (tmm160) cc_final: 0.7333 (tmm-80) REVERT: C 83 MET cc_start: 0.6356 (mmm) cc_final: 0.6123 (mmp) REVERT: C 93 VAL cc_start: 0.8576 (m) cc_final: 0.8206 (p) REVERT: C 94 TYR cc_start: 0.5318 (m-10) cc_final: 0.4850 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2369 time to fit residues: 74.2638 Evaluate side-chains 154 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 122 optimal weight: 0.0020 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.118176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091692 restraints weight = 26734.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093548 restraints weight = 17523.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094127 restraints weight = 12466.610| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10402 Z= 0.124 Angle : 0.619 7.663 14115 Z= 0.303 Chirality : 0.041 0.183 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.936 62.955 1483 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.03 (0.24), residues: 1276 helix: 1.62 (0.18), residues: 777 sheet: -0.23 (0.43), residues: 130 loop : -0.94 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 PHE 0.016 0.001 PHE A 478 TYR 0.023 0.001 TYR B 187 ARG 0.003 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 634) hydrogen bonds : angle 3.99915 ( 1863) SS BOND : bond 0.00790 ( 2) SS BOND : angle 1.79414 ( 4) covalent geometry : bond 0.00275 (10400) covalent geometry : angle 0.61801 (14111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8815 (t0) cc_final: 0.8252 (t70) REVERT: A 299 TYR cc_start: 0.8957 (m-80) cc_final: 0.8379 (m-80) REVERT: A 376 LEU cc_start: 0.6446 (mt) cc_final: 0.6089 (mt) REVERT: A 444 PHE cc_start: 0.7161 (t80) cc_final: 0.6752 (t80) REVERT: A 455 ARG cc_start: 0.7648 (ptt-90) cc_final: 0.7413 (ptt-90) REVERT: B 32 LEU cc_start: 0.8209 (mt) cc_final: 0.7692 (mt) REVERT: B 79 MET cc_start: 0.8854 (tmm) cc_final: 0.8615 (tmm) REVERT: B 154 MET cc_start: 0.8649 (ttt) cc_final: 0.8132 (ttp) REVERT: B 199 THR cc_start: 0.8971 (m) cc_final: 0.8597 (m) REVERT: B 365 MET cc_start: 0.8079 (tmm) cc_final: 0.7842 (tmm) REVERT: B 380 LEU cc_start: 0.8545 (tp) cc_final: 0.8331 (tp) REVERT: B 436 LEU cc_start: 0.8840 (tp) cc_final: 0.8571 (tp) REVERT: B 559 LEU cc_start: 0.9333 (mt) cc_final: 0.9102 (mt) REVERT: B 569 MET cc_start: 0.6978 (ttm) cc_final: 0.6279 (ttm) REVERT: C 65 LYS cc_start: 0.8963 (ptmt) cc_final: 0.8602 (mttm) REVERT: C 72 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7420 (tmm-80) REVERT: C 83 MET cc_start: 0.6192 (mmm) cc_final: 0.5760 (mmp) REVERT: C 93 VAL cc_start: 0.8775 (m) cc_final: 0.8381 (p) REVERT: C 94 TYR cc_start: 0.5542 (m-10) cc_final: 0.5087 (m-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2238 time to fit residues: 67.6517 Evaluate side-chains 156 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN B 538 HIS ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091370 restraints weight = 26629.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092845 restraints weight = 17472.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093445 restraints weight = 12977.400| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10402 Z= 0.129 Angle : 0.637 7.866 14115 Z= 0.313 Chirality : 0.041 0.199 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.737 56.787 1483 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 1.09 (0.24), residues: 1276 helix: 1.64 (0.18), residues: 780 sheet: -0.40 (0.42), residues: 137 loop : -0.79 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 PHE 0.019 0.001 PHE B 163 TYR 0.022 0.001 TYR B 187 ARG 0.005 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 634) hydrogen bonds : angle 4.02437 ( 1863) SS BOND : bond 0.00763 ( 2) SS BOND : angle 1.56761 ( 4) covalent geometry : bond 0.00290 (10400) covalent geometry : angle 0.63676 (14111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8768 (t0) cc_final: 0.8281 (t70) REVERT: A 209 LEU cc_start: 0.8953 (tt) cc_final: 0.8734 (tp) REVERT: A 299 TYR cc_start: 0.8933 (m-80) cc_final: 0.8441 (m-80) REVERT: A 376 LEU cc_start: 0.6518 (mt) cc_final: 0.6242 (mt) REVERT: A 417 VAL cc_start: 0.5506 (t) cc_final: 0.5264 (t) REVERT: A 444 PHE cc_start: 0.7226 (t80) cc_final: 0.6813 (t80) REVERT: A 544 MET cc_start: 0.7272 (mmt) cc_final: 0.6744 (mmm) REVERT: B 32 LEU cc_start: 0.8253 (mt) cc_final: 0.7695 (mt) REVERT: B 79 MET cc_start: 0.8824 (tmm) cc_final: 0.8568 (tmm) REVERT: B 154 MET cc_start: 0.8712 (ttt) cc_final: 0.8083 (ttp) REVERT: B 199 THR cc_start: 0.8993 (m) cc_final: 0.8643 (m) REVERT: B 365 MET cc_start: 0.8107 (tmm) cc_final: 0.7822 (tmm) REVERT: B 380 LEU cc_start: 0.8561 (tp) cc_final: 0.8340 (tp) REVERT: B 436 LEU cc_start: 0.8876 (tp) cc_final: 0.8576 (tp) REVERT: B 559 LEU cc_start: 0.9379 (mt) cc_final: 0.9159 (mt) REVERT: B 569 MET cc_start: 0.7190 (ttm) cc_final: 0.6849 (ttm) REVERT: C 65 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8540 (mttt) REVERT: C 72 ARG cc_start: 0.7848 (tmm160) cc_final: 0.7477 (tmm-80) REVERT: C 83 MET cc_start: 0.6470 (mmm) cc_final: 0.5985 (mmp) REVERT: C 93 VAL cc_start: 0.8687 (m) cc_final: 0.8328 (p) REVERT: C 94 TYR cc_start: 0.5600 (m-10) cc_final: 0.5110 (m-80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2185 time to fit residues: 63.1227 Evaluate side-chains 150 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091174 restraints weight = 26621.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093630 restraints weight = 16853.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095295 restraints weight = 12377.121| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10402 Z= 0.118 Angle : 0.623 7.960 14115 Z= 0.305 Chirality : 0.041 0.178 1609 Planarity : 0.004 0.046 1785 Dihedral : 4.524 53.801 1483 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.24), residues: 1276 helix: 1.75 (0.18), residues: 780 sheet: -0.39 (0.42), residues: 138 loop : -0.72 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 PHE 0.017 0.001 PHE A 478 TYR 0.019 0.001 TYR B 302 ARG 0.004 0.000 ARG B 471 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 634) hydrogen bonds : angle 3.91266 ( 1863) SS BOND : bond 0.00810 ( 2) SS BOND : angle 1.60625 ( 4) covalent geometry : bond 0.00254 (10400) covalent geometry : angle 0.62271 (14111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8797 (t0) cc_final: 0.8302 (t70) REVERT: A 299 TYR cc_start: 0.8890 (m-80) cc_final: 0.8405 (m-80) REVERT: A 444 PHE cc_start: 0.7198 (t80) cc_final: 0.6850 (t80) REVERT: A 544 MET cc_start: 0.7272 (mmt) cc_final: 0.6745 (mmm) REVERT: B 32 LEU cc_start: 0.8237 (mt) cc_final: 0.7713 (mt) REVERT: B 79 MET cc_start: 0.8806 (tmm) cc_final: 0.8531 (tmm) REVERT: B 154 MET cc_start: 0.8536 (ttt) cc_final: 0.7934 (ttp) REVERT: B 191 GLN cc_start: 0.8576 (mp-120) cc_final: 0.8145 (mp10) REVERT: B 199 THR cc_start: 0.9000 (m) cc_final: 0.8664 (m) REVERT: B 365 MET cc_start: 0.8007 (tmm) cc_final: 0.7788 (tmm) REVERT: B 380 LEU cc_start: 0.8509 (tp) cc_final: 0.8303 (tp) REVERT: B 436 LEU cc_start: 0.8805 (tp) cc_final: 0.8524 (tp) REVERT: B 559 LEU cc_start: 0.9319 (mt) cc_final: 0.9064 (mt) REVERT: B 569 MET cc_start: 0.7074 (ttm) cc_final: 0.6731 (ttm) REVERT: C 65 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8502 (mttt) REVERT: C 72 ARG cc_start: 0.7847 (tmm160) cc_final: 0.7553 (tmm-80) REVERT: C 83 MET cc_start: 0.6722 (mmm) cc_final: 0.6363 (mmp) REVERT: C 93 VAL cc_start: 0.8754 (m) cc_final: 0.8373 (p) REVERT: C 94 TYR cc_start: 0.5884 (m-10) cc_final: 0.5468 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2267 time to fit residues: 67.0509 Evaluate side-chains 157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 116 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.119697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092363 restraints weight = 26856.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094923 restraints weight = 16420.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096669 restraints weight = 11752.200| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10402 Z= 0.115 Angle : 0.626 8.126 14115 Z= 0.304 Chirality : 0.041 0.178 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.373 51.891 1483 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.24), residues: 1276 helix: 1.85 (0.18), residues: 776 sheet: -0.26 (0.42), residues: 142 loop : -0.73 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 36 HIS 0.002 0.001 HIS B 101 PHE 0.022 0.001 PHE B 163 TYR 0.019 0.001 TYR B 187 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 634) hydrogen bonds : angle 3.89939 ( 1863) SS BOND : bond 0.00712 ( 2) SS BOND : angle 1.53751 ( 4) covalent geometry : bond 0.00248 (10400) covalent geometry : angle 0.62528 (14111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8822 (t0) cc_final: 0.8277 (t70) REVERT: A 299 TYR cc_start: 0.8886 (m-80) cc_final: 0.8443 (m-80) REVERT: A 444 PHE cc_start: 0.7316 (t80) cc_final: 0.6877 (t80) REVERT: A 455 ARG cc_start: 0.7495 (ptt-90) cc_final: 0.6911 (ptp90) REVERT: A 544 MET cc_start: 0.7240 (mmt) cc_final: 0.6827 (mmm) REVERT: B 32 LEU cc_start: 0.8218 (mt) cc_final: 0.7705 (mt) REVERT: B 79 MET cc_start: 0.8861 (tmm) cc_final: 0.8581 (tmm) REVERT: B 154 MET cc_start: 0.8739 (ttt) cc_final: 0.8395 (ttt) REVERT: B 191 GLN cc_start: 0.8604 (mp-120) cc_final: 0.8244 (mp10) REVERT: B 199 THR cc_start: 0.8976 (m) cc_final: 0.8649 (m) REVERT: B 347 LYS cc_start: 0.6759 (tptt) cc_final: 0.6252 (tppt) REVERT: B 365 MET cc_start: 0.8127 (tmm) cc_final: 0.7851 (tmm) REVERT: B 380 LEU cc_start: 0.8487 (tp) cc_final: 0.8272 (tp) REVERT: B 436 LEU cc_start: 0.8883 (tp) cc_final: 0.8525 (tp) REVERT: B 559 LEU cc_start: 0.9293 (mt) cc_final: 0.9029 (mt) REVERT: B 569 MET cc_start: 0.7088 (ttm) cc_final: 0.6732 (ttm) REVERT: C 65 LYS cc_start: 0.9007 (ptmt) cc_final: 0.8706 (mttt) REVERT: C 72 ARG cc_start: 0.7899 (tmm160) cc_final: 0.7620 (tmm-80) REVERT: C 83 MET cc_start: 0.6422 (mmm) cc_final: 0.5862 (mmp) REVERT: C 93 VAL cc_start: 0.8722 (m) cc_final: 0.8319 (p) REVERT: C 94 TYR cc_start: 0.6135 (m-10) cc_final: 0.5655 (m-80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2154 time to fit residues: 61.7991 Evaluate side-chains 152 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090186 restraints weight = 26851.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092652 restraints weight = 16548.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094275 restraints weight = 11999.024| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10402 Z= 0.136 Angle : 0.636 8.165 14115 Z= 0.312 Chirality : 0.042 0.174 1609 Planarity : 0.004 0.045 1785 Dihedral : 4.370 52.334 1483 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.32 (0.24), residues: 1276 helix: 1.88 (0.18), residues: 771 sheet: -0.44 (0.42), residues: 137 loop : -0.70 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 36 HIS 0.004 0.001 HIS B 101 PHE 0.018 0.001 PHE A 478 TYR 0.020 0.001 TYR B 187 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 634) hydrogen bonds : angle 4.00249 ( 1863) SS BOND : bond 0.00744 ( 2) SS BOND : angle 1.60667 ( 4) covalent geometry : bond 0.00307 (10400) covalent geometry : angle 0.63522 (14111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.27 seconds wall clock time: 72 minutes 24.03 seconds (4344.03 seconds total)