Starting phenix.real_space_refine on Thu Jul 31 07:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.map" model { file = "/net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a2g_11624/07_2025/7a2g_11624.cif" } resolution = 4.1 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= 0.008 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 40 5.16 5 C 8520 2.51 5 N 2344 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.74, per 1000 atoms: 0.65 Number of scatterers: 13408 At special positions: 0 Unit cell: (101.85, 119.7, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 40 16.00 O 2500 8.00 N 2344 7.00 C 8520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 16 sheets defined 50.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.991A pdb=" N VAL A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.188A pdb=" N VAL A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.080A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.705A pdb=" N ALA A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.743A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.603A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.930A pdb=" N VAL B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.574A pdb=" N VAL B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 225 through 244 removed outlier: 4.542A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 271 through 283 removed outlier: 4.212A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.051A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 396 through 404 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 471 through 496 removed outlier: 3.688A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.886A pdb=" N VAL C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 3.558A pdb=" N VAL C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 174 through 182 removed outlier: 3.829A pdb=" N VAL C 180 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 225 through 244 removed outlier: 4.303A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 271 through 284 removed outlier: 4.286A pdb=" N VAL C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.841A pdb=" N LEU C 333 " --> pdb=" O CYS C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 356 removed outlier: 3.632A pdb=" N LEU C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 396 through 404 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.769A pdb=" N VAL C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.971A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.931A pdb=" N VAL D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.522A pdb=" N VAL D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.778A pdb=" N VAL D 180 " --> pdb=" O CYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 225 through 244 removed outlier: 4.027A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 262 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 295 through 305 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.508A pdb=" N LEU D 333 " --> pdb=" O CYS D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 355 removed outlier: 3.667A pdb=" N SER D 355 " --> pdb=" O ILE D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 396 through 404 Processing helix chain 'D' and resid 413 through 419 removed outlier: 4.120A pdb=" N VAL D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 471 through 496 removed outlier: 3.747A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.483A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 411 removed outlier: 6.928A pdb=" N ARG A 410 " --> pdb=" O VAL A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 459 Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.426A pdb=" N GLN B 286 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B 310 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 288 " --> pdb=" O CYS B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AA7, first strand: chain 'B' and resid 409 through 411 removed outlier: 6.980A pdb=" N ARG B 410 " --> pdb=" O VAL B 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 456 through 459 Processing sheet with id=AA9, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.137A pdb=" N GLN C 286 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS C 310 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 288 " --> pdb=" O CYS C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 409 through 411 removed outlier: 6.959A pdb=" N ARG C 410 " --> pdb=" O VAL C 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 456 through 459 Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.225A pdb=" N GLN D 286 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS D 310 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG D 288 " --> pdb=" O CYS D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 378 through 381 Processing sheet with id=AB6, first strand: chain 'D' and resid 409 through 411 removed outlier: 6.907A pdb=" N ARG D 410 " --> pdb=" O VAL D 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 456 through 459 588 hydrogen bonds defined for protein. 1728 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: 3.93 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4370 1.33 - 1.45: 2195 1.45 - 1.57: 7123 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 13740 Sorted by residual: bond pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 1.541 1.515 0.027 1.24e-02 6.50e+03 4.62e+00 bond pdb=" CA ILE B 219 " pdb=" CB ILE B 219 " ideal model delta sigma weight residual 1.540 1.515 0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" CA ILE C 219 " pdb=" CB ILE C 219 " ideal model delta sigma weight residual 1.540 1.518 0.022 1.23e-02 6.61e+03 3.28e+00 bond pdb=" C ARG C 120 " pdb=" N PRO C 121 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" N SER C 323 " pdb=" CA SER C 323 " ideal model delta sigma weight residual 1.458 1.439 0.020 1.25e-02 6.40e+03 2.51e+00 ... (remaining 13735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18015 2.03 - 4.06: 530 4.06 - 6.09: 61 6.09 - 8.11: 17 8.11 - 10.14: 1 Bond angle restraints: 18624 Sorted by residual: angle pdb=" N SER A 394 " pdb=" CA SER A 394 " pdb=" C SER A 394 " ideal model delta sigma weight residual 114.31 107.90 6.41 1.29e+00 6.01e-01 2.47e+01 angle pdb=" N SER B 394 " pdb=" CA SER B 394 " pdb=" C SER B 394 " ideal model delta sigma weight residual 113.97 107.86 6.11 1.28e+00 6.10e-01 2.28e+01 angle pdb=" N GLY D 263 " pdb=" CA GLY D 263 " pdb=" C GLY D 263 " ideal model delta sigma weight residual 115.63 109.80 5.83 1.49e+00 4.50e-01 1.53e+01 angle pdb=" N VAL A 136 " pdb=" CA VAL A 136 " pdb=" C VAL A 136 " ideal model delta sigma weight residual 108.53 104.36 4.17 1.22e+00 6.72e-01 1.17e+01 angle pdb=" C ALA A 95 " pdb=" N LEU A 96 " pdb=" CA LEU A 96 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 ... (remaining 18619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7310 17.72 - 35.43: 813 35.43 - 53.15: 124 53.15 - 70.87: 20 70.87 - 88.58: 17 Dihedral angle restraints: 8284 sinusoidal: 3368 harmonic: 4916 Sorted by residual: dihedral pdb=" CA VAL D 163 " pdb=" C VAL D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta harmonic sigma weight residual -180.00 -146.80 -33.20 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA VAL C 163 " pdb=" C VAL C 163 " pdb=" N PRO C 164 " pdb=" CA PRO C 164 " ideal model delta harmonic sigma weight residual -180.00 -147.11 -32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA LEU C 293 " pdb=" C LEU C 293 " pdb=" N LEU C 294 " pdb=" CA LEU C 294 " ideal model delta harmonic sigma weight residual -180.00 -147.68 -32.32 0 5.00e+00 4.00e-02 4.18e+01 ... (remaining 8281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1337 0.041 - 0.081: 525 0.081 - 0.122: 118 0.122 - 0.162: 18 0.162 - 0.203: 2 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CG LEU A 393 " pdb=" CB LEU A 393 " pdb=" CD1 LEU A 393 " pdb=" CD2 LEU A 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU C 189 " pdb=" CB LEU C 189 " pdb=" CD1 LEU C 189 " pdb=" CD2 LEU C 189 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1997 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 164 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 413 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 414 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 164 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.028 5.00e-02 4.00e+02 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 342 2.47 - 3.08: 11983 3.08 - 3.69: 25480 3.69 - 4.29: 34407 4.29 - 4.90: 49923 Nonbonded interactions: 122135 Sorted by model distance: nonbonded pdb=" OE2 GLU B 375 " pdb="FE FE B 501 " model vdw 1.869 2.260 nonbonded pdb="FE FE D 501 " pdb=" O HOH D 601 " model vdw 1.873 2.260 nonbonded pdb="FE FE B 501 " pdb=" O HOH B 601 " model vdw 1.876 2.260 nonbonded pdb="FE FE A 501 " pdb=" O HOH A 601 " model vdw 1.891 2.260 nonbonded pdb=" NE2 HIS B 335 " pdb="FE FE B 501 " model vdw 1.908 2.340 ... (remaining 122130 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.890 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:3.070 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.006 0.045 13740 Z= 0.319 Angle : 0.858 10.143 18624 Z= 0.514 Chirality : 0.044 0.203 2000 Planarity : 0.006 0.063 2456 Dihedral : 15.223 88.583 5108 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 47.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.33 % Favored : 83.43 % Rotamer: Outliers : 0.49 % Allowed : 9.24 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.19 % 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: -5.55 (0.15), residues: 1672 helix: -2.79 (0.14), residues: 764 sheet: -3.64 (0.35), residues: 152 loop : -4.72 (0.16), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 165 HIS 0.018 0.003 HIS B 111 PHE 0.024 0.002 PHE D 194 TYR 0.020 0.002 TYR A 243 ARG 0.004 0.001 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.21519 ( 588) hydrogen bonds : angle 7.90519 ( 1728) covalent geometry : bond 0.00569 (13740) covalent geometry : angle 0.85757 (18624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 1.861 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7757 (pmm) cc_final: 0.7329 (ppp) REVERT: A 135 GLU cc_start: 0.9407 (tt0) cc_final: 0.9151 (tt0) REVERT: A 303 LEU cc_start: 0.9340 (mm) cc_final: 0.9051 (mm) REVERT: B 81 MET cc_start: 0.7252 (pmm) cc_final: 0.6554 (ppp) REVERT: B 338 MET cc_start: 0.8941 (mmt) cc_final: 0.8418 (mmt) REVERT: B 344 PHE cc_start: 0.9327 (t80) cc_final: 0.8894 (t80) REVERT: B 388 TYR cc_start: 0.9202 (p90) cc_final: 0.8640 (p90) REVERT: B 458 LYS cc_start: 0.9687 (tmtt) cc_final: 0.9267 (tptt) REVERT: B 484 ASP cc_start: 0.9610 (t0) cc_final: 0.9324 (t0) REVERT: B 487 ASP cc_start: 0.9505 (t0) cc_final: 0.9256 (p0) REVERT: C 81 MET cc_start: 0.7508 (pmm) cc_final: 0.6967 (ppp) REVERT: C 349 GLN cc_start: 0.9005 (tt0) cc_final: 0.8794 (tt0) REVERT: D 81 MET cc_start: 0.7730 (pmm) cc_final: 0.7303 (ppp) REVERT: D 138 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.8005 (mmm160) REVERT: D 329 CYS cc_start: 0.9457 (m) cc_final: 0.9117 (m) REVERT: D 333 LEU cc_start: 0.9497 (mm) cc_final: 0.8941 (tp) REVERT: D 344 PHE cc_start: 0.9475 (t80) cc_final: 0.9267 (t80) REVERT: D 441 LYS cc_start: 0.9302 (ttmt) cc_final: 0.9080 (tttp) outliers start: 7 outliers final: 3 residues processed: 214 average time/residue: 0.2994 time to fit residues: 88.8227 Evaluate side-chains 165 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS C 83 ASN C 111 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 428 GLN C 483 GLN D 111 HIS ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 349 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.073542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048351 restraints weight = 65506.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049960 restraints weight = 47365.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.051136 restraints weight = 35959.144| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13740 Z= 0.194 Angle : 0.770 8.031 18624 Z= 0.400 Chirality : 0.044 0.173 2000 Planarity : 0.006 0.046 2456 Dihedral : 5.903 31.105 1868 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 0.42 % Allowed : 8.26 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.00 % 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: -3.92 (0.18), residues: 1672 helix: -1.23 (0.16), residues: 796 sheet: -4.46 (0.36), residues: 104 loop : -3.94 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 165 HIS 0.013 0.002 HIS B 111 PHE 0.021 0.002 PHE C 347 TYR 0.016 0.002 TYR B 213 ARG 0.005 0.001 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.06284 ( 588) hydrogen bonds : angle 6.39774 ( 1728) covalent geometry : bond 0.00389 (13740) covalent geometry : angle 0.77045 (18624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 1.513 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7685 (pmm) cc_final: 0.7410 (ppp) REVERT: A 166 PHE cc_start: 0.9524 (p90) cc_final: 0.9154 (p90) REVERT: A 208 GLU cc_start: 0.9564 (pt0) cc_final: 0.9167 (pp20) REVERT: A 277 ARG cc_start: 0.9403 (ttm170) cc_final: 0.9085 (mtt180) REVERT: A 281 GLU cc_start: 0.9775 (mm-30) cc_final: 0.9479 (mm-30) REVERT: A 303 LEU cc_start: 0.9369 (mm) cc_final: 0.9085 (mm) REVERT: A 445 ARG cc_start: 0.9652 (ptt90) cc_final: 0.9427 (ptt90) REVERT: B 81 MET cc_start: 0.7288 (pmm) cc_final: 0.6944 (ppp) REVERT: B 344 PHE cc_start: 0.9320 (t80) cc_final: 0.8697 (t80) REVERT: B 347 PHE cc_start: 0.9210 (t80) cc_final: 0.8917 (t80) REVERT: B 349 GLN cc_start: 0.9546 (tt0) cc_final: 0.9343 (tt0) REVERT: B 388 TYR cc_start: 0.9122 (p90) cc_final: 0.8582 (p90) REVERT: B 441 LYS cc_start: 0.9519 (mtmm) cc_final: 0.9272 (mttt) REVERT: B 487 ASP cc_start: 0.9552 (t0) cc_final: 0.9315 (p0) REVERT: C 81 MET cc_start: 0.7435 (pmm) cc_final: 0.7020 (ppp) REVERT: C 208 GLU cc_start: 0.9635 (pt0) cc_final: 0.9298 (pp20) REVERT: C 303 LEU cc_start: 0.9523 (mm) cc_final: 0.9221 (mm) REVERT: C 388 TYR cc_start: 0.8931 (p90) cc_final: 0.8634 (p90) REVERT: C 458 LYS cc_start: 0.9597 (tmtt) cc_final: 0.9316 (tmtt) REVERT: C 467 ASP cc_start: 0.9049 (m-30) cc_final: 0.7263 (m-30) REVERT: D 81 MET cc_start: 0.7521 (pmm) cc_final: 0.7179 (ppp) REVERT: D 173 LEU cc_start: 0.9745 (mm) cc_final: 0.9533 (mm) REVERT: D 344 PHE cc_start: 0.9532 (t80) cc_final: 0.9088 (t80) REVERT: D 347 PHE cc_start: 0.9635 (t80) cc_final: 0.9035 (t80) REVERT: D 441 LYS cc_start: 0.9469 (ttmt) cc_final: 0.9020 (ttmt) outliers start: 6 outliers final: 1 residues processed: 226 average time/residue: 0.2981 time to fit residues: 94.9555 Evaluate side-chains 165 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 49 optimal weight: 40.0000 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.074136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049627 restraints weight = 67205.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051230 restraints weight = 48200.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052462 restraints weight = 36470.664| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13740 Z= 0.219 Angle : 0.753 7.217 18624 Z= 0.393 Chirality : 0.044 0.188 2000 Planarity : 0.006 0.053 2456 Dihedral : 5.767 31.226 1868 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -3.24 (0.19), residues: 1672 helix: -0.57 (0.17), residues: 792 sheet: -4.48 (0.35), residues: 104 loop : -3.63 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 165 HIS 0.017 0.002 HIS B 111 PHE 0.025 0.002 PHE C 347 TYR 0.043 0.002 TYR A 243 ARG 0.005 0.000 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.05689 ( 588) hydrogen bonds : angle 6.20140 ( 1728) covalent geometry : bond 0.00431 (13740) covalent geometry : angle 0.75336 (18624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.494 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8091 (pmm) cc_final: 0.7689 (ppp) REVERT: A 178 HIS cc_start: 0.9151 (m-70) cc_final: 0.8946 (m-70) REVERT: A 208 GLU cc_start: 0.9549 (pt0) cc_final: 0.9167 (pp20) REVERT: A 277 ARG cc_start: 0.9421 (ttm170) cc_final: 0.9049 (mmt180) REVERT: A 281 GLU cc_start: 0.9789 (mm-30) cc_final: 0.9491 (mm-30) REVERT: A 303 LEU cc_start: 0.9403 (mm) cc_final: 0.9131 (mm) REVERT: A 331 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8578 (pt0) REVERT: A 441 LYS cc_start: 0.9446 (tttp) cc_final: 0.9133 (mttm) REVERT: A 458 LYS cc_start: 0.9726 (tmtt) cc_final: 0.9487 (tmtt) REVERT: B 81 MET cc_start: 0.7636 (pmm) cc_final: 0.7083 (ppp) REVERT: B 331 GLU cc_start: 0.8563 (pt0) cc_final: 0.8333 (pt0) REVERT: B 344 PHE cc_start: 0.9394 (t80) cc_final: 0.8994 (t80) REVERT: B 347 PHE cc_start: 0.9270 (t80) cc_final: 0.8919 (t80) REVERT: B 349 GLN cc_start: 0.9510 (tt0) cc_final: 0.9030 (tm-30) REVERT: B 353 LEU cc_start: 0.9465 (mt) cc_final: 0.8582 (mt) REVERT: B 441 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9229 (mttt) REVERT: B 444 LEU cc_start: 0.9320 (tt) cc_final: 0.9074 (tt) REVERT: B 458 LYS cc_start: 0.9692 (tmtt) cc_final: 0.9448 (tmtt) REVERT: B 484 ASP cc_start: 0.9640 (t70) cc_final: 0.9392 (t0) REVERT: B 487 ASP cc_start: 0.9563 (t0) cc_final: 0.9300 (p0) REVERT: C 81 MET cc_start: 0.7573 (pmm) cc_final: 0.7148 (ppp) REVERT: C 208 GLU cc_start: 0.9685 (pt0) cc_final: 0.9375 (pp20) REVERT: C 331 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8397 (pt0) REVERT: C 344 PHE cc_start: 0.9362 (t80) cc_final: 0.9113 (t80) REVERT: C 349 GLN cc_start: 0.9250 (tt0) cc_final: 0.8523 (tm-30) REVERT: C 353 LEU cc_start: 0.9527 (mt) cc_final: 0.8824 (mt) REVERT: C 458 LYS cc_start: 0.9655 (tmtt) cc_final: 0.9414 (tmtt) REVERT: C 469 LEU cc_start: 0.8992 (mt) cc_final: 0.8644 (mt) REVERT: D 81 MET cc_start: 0.7450 (pmm) cc_final: 0.7164 (ppp) REVERT: D 329 CYS cc_start: 0.9302 (m) cc_final: 0.8868 (m) REVERT: D 333 LEU cc_start: 0.9486 (mm) cc_final: 0.8830 (tp) REVERT: D 344 PHE cc_start: 0.9553 (t80) cc_final: 0.9152 (t80) REVERT: D 347 PHE cc_start: 0.9559 (t80) cc_final: 0.8948 (t80) REVERT: D 441 LYS cc_start: 0.9450 (ttmt) cc_final: 0.9013 (ttmt) REVERT: D 444 LEU cc_start: 0.9376 (tt) cc_final: 0.8912 (tt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2864 time to fit residues: 84.9360 Evaluate side-chains 157 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.075821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049658 restraints weight = 68859.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051364 restraints weight = 48951.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052607 restraints weight = 37008.724| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13740 Z= 0.177 Angle : 0.725 7.880 18624 Z= 0.373 Chirality : 0.044 0.229 2000 Planarity : 0.005 0.067 2456 Dihedral : 5.578 30.340 1868 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -2.88 (0.19), residues: 1672 helix: -0.29 (0.17), residues: 796 sheet: -4.36 (0.36), residues: 104 loop : -3.42 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 165 HIS 0.016 0.002 HIS B 111 PHE 0.033 0.002 PHE A 305 TYR 0.041 0.002 TYR A 243 ARG 0.006 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 588) hydrogen bonds : angle 5.99326 ( 1728) covalent geometry : bond 0.00360 (13740) covalent geometry : angle 0.72524 (18624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.494 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7879 (pmm) cc_final: 0.7587 (ppp) REVERT: A 208 GLU cc_start: 0.9554 (pt0) cc_final: 0.9174 (pp20) REVERT: A 303 LEU cc_start: 0.9390 (mm) cc_final: 0.9087 (mm) REVERT: A 331 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8484 (pt0) REVERT: A 441 LYS cc_start: 0.9517 (ttmm) cc_final: 0.9055 (mtpt) REVERT: B 81 MET cc_start: 0.7441 (pmm) cc_final: 0.7057 (ppp) REVERT: B 347 PHE cc_start: 0.9310 (t80) cc_final: 0.9072 (t80) REVERT: B 441 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9185 (mttt) REVERT: B 444 LEU cc_start: 0.9180 (tt) cc_final: 0.8975 (tt) REVERT: B 458 LYS cc_start: 0.9708 (tmtt) cc_final: 0.9465 (tmtt) REVERT: B 484 ASP cc_start: 0.9623 (t70) cc_final: 0.9364 (t0) REVERT: B 487 ASP cc_start: 0.9552 (t0) cc_final: 0.9286 (p0) REVERT: C 81 MET cc_start: 0.7384 (pmm) cc_final: 0.7034 (ppp) REVERT: C 208 GLU cc_start: 0.9689 (pt0) cc_final: 0.9371 (pp20) REVERT: C 331 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 344 PHE cc_start: 0.9413 (t80) cc_final: 0.8942 (t80) REVERT: C 347 PHE cc_start: 0.9313 (t80) cc_final: 0.8880 (t80) REVERT: C 444 LEU cc_start: 0.9112 (tt) cc_final: 0.8849 (tt) REVERT: C 458 LYS cc_start: 0.9718 (tmtt) cc_final: 0.9454 (tmtt) REVERT: C 460 ASP cc_start: 0.8920 (t70) cc_final: 0.8323 (t0) REVERT: C 469 LEU cc_start: 0.8964 (mt) cc_final: 0.8648 (mt) REVERT: D 81 MET cc_start: 0.7378 (pmm) cc_final: 0.7148 (ppp) REVERT: D 232 TRP cc_start: 0.8548 (t-100) cc_final: 0.8341 (t-100) REVERT: D 329 CYS cc_start: 0.9287 (m) cc_final: 0.8878 (m) REVERT: D 333 LEU cc_start: 0.9529 (mm) cc_final: 0.8962 (tp) REVERT: D 344 PHE cc_start: 0.9586 (t80) cc_final: 0.9229 (t80) REVERT: D 347 PHE cc_start: 0.9560 (t80) cc_final: 0.8937 (t80) REVERT: D 441 LYS cc_start: 0.9491 (ttmt) cc_final: 0.9077 (ttmt) REVERT: D 444 LEU cc_start: 0.9410 (tt) cc_final: 0.8949 (tt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2747 time to fit residues: 82.6510 Evaluate side-chains 155 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 167 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS B 349 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.080250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.053931 restraints weight = 66103.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055657 restraints weight = 46939.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056898 restraints weight = 35684.486| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13740 Z= 0.138 Angle : 0.715 8.117 18624 Z= 0.363 Chirality : 0.044 0.177 2000 Planarity : 0.005 0.045 2456 Dihedral : 5.369 28.680 1868 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 0.07 % Allowed : 2.94 % Favored : 96.99 % 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: -2.58 (0.20), residues: 1672 helix: -0.01 (0.18), residues: 800 sheet: -4.24 (0.37), residues: 104 loop : -3.32 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 165 HIS 0.010 0.001 HIS B 111 PHE 0.027 0.002 PHE A 285 TYR 0.041 0.001 TYR A 243 ARG 0.004 0.000 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 588) hydrogen bonds : angle 5.66894 ( 1728) covalent geometry : bond 0.00290 (13740) covalent geometry : angle 0.71487 (18624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.513 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7929 (pmm) cc_final: 0.7594 (ppp) REVERT: A 166 PHE cc_start: 0.9679 (p90) cc_final: 0.9344 (p90) REVERT: A 168 ARG cc_start: 0.9266 (mmm160) cc_final: 0.8879 (mmm160) REVERT: A 208 GLU cc_start: 0.9527 (pt0) cc_final: 0.9168 (pp20) REVERT: A 303 LEU cc_start: 0.9273 (mm) cc_final: 0.8987 (mm) REVERT: A 331 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8318 (pt0) REVERT: A 441 LYS cc_start: 0.9502 (ttmm) cc_final: 0.9070 (mtpt) REVERT: B 81 MET cc_start: 0.7593 (pmm) cc_final: 0.7187 (ppp) REVERT: B 232 TRP cc_start: 0.8782 (t-100) cc_final: 0.8394 (t-100) REVERT: B 329 CYS cc_start: 0.9391 (m) cc_final: 0.9070 (m) REVERT: B 333 LEU cc_start: 0.9414 (mm) cc_final: 0.8781 (tp) REVERT: B 466 ILE cc_start: 0.9313 (mt) cc_final: 0.9048 (mt) REVERT: B 484 ASP cc_start: 0.9638 (t70) cc_final: 0.9315 (t0) REVERT: B 487 ASP cc_start: 0.9571 (t0) cc_final: 0.9323 (p0) REVERT: C 81 MET cc_start: 0.7407 (pmm) cc_final: 0.7033 (ppp) REVERT: C 208 GLU cc_start: 0.9654 (pt0) cc_final: 0.9337 (pp20) REVERT: C 344 PHE cc_start: 0.9391 (t80) cc_final: 0.9103 (t80) REVERT: C 347 PHE cc_start: 0.9262 (t80) cc_final: 0.8829 (t80) REVERT: C 458 LYS cc_start: 0.9727 (tmtt) cc_final: 0.9471 (tmtt) REVERT: C 460 ASP cc_start: 0.8932 (t70) cc_final: 0.8249 (t0) REVERT: C 466 ILE cc_start: 0.9667 (mt) cc_final: 0.9235 (mt) REVERT: C 469 LEU cc_start: 0.9017 (mt) cc_final: 0.8698 (mt) REVERT: D 81 MET cc_start: 0.7400 (pmm) cc_final: 0.7172 (ppp) REVERT: D 329 CYS cc_start: 0.9165 (m) cc_final: 0.8811 (m) REVERT: D 333 LEU cc_start: 0.9520 (mm) cc_final: 0.8962 (tp) REVERT: D 347 PHE cc_start: 0.9554 (t80) cc_final: 0.8975 (t80) REVERT: D 441 LYS cc_start: 0.9516 (ttmt) cc_final: 0.9139 (ttmt) REVERT: D 467 ASP cc_start: 0.9152 (m-30) cc_final: 0.8223 (m-30) REVERT: D 469 LEU cc_start: 0.9440 (mt) cc_final: 0.9190 (mt) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.2793 time to fit residues: 87.1595 Evaluate side-chains 155 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 50 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 chunk 126 optimal weight: 50.0000 chunk 149 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.076663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051399 restraints weight = 67996.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053025 restraints weight = 49669.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054133 restraints weight = 38496.901| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13740 Z= 0.220 Angle : 0.747 8.175 18624 Z= 0.388 Chirality : 0.044 0.160 2000 Planarity : 0.005 0.048 2456 Dihedral : 5.483 30.742 1868 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -2.46 (0.20), residues: 1672 helix: 0.04 (0.18), residues: 800 sheet: -4.32 (0.50), residues: 56 loop : -3.31 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 165 HIS 0.008 0.002 HIS A 251 PHE 0.024 0.002 PHE A 285 TYR 0.017 0.002 TYR A 427 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 588) hydrogen bonds : angle 6.04907 ( 1728) covalent geometry : bond 0.00435 (13740) covalent geometry : angle 0.74721 (18624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.535 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: symmetry clash REVERT: A 81 MET cc_start: 0.8093 (pmm) cc_final: 0.7711 (ppp) REVERT: A 168 ARG cc_start: 0.9179 (mmm160) cc_final: 0.8949 (mmm-85) REVERT: A 178 HIS cc_start: 0.9066 (m-70) cc_final: 0.8806 (m-70) REVERT: A 303 LEU cc_start: 0.9302 (mm) cc_final: 0.8966 (mm) REVERT: A 331 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8551 (pt0) REVERT: A 347 PHE cc_start: 0.9570 (t80) cc_final: 0.9188 (t80) REVERT: A 441 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9093 (mtpt) REVERT: A 458 LYS cc_start: 0.9760 (tmtt) cc_final: 0.9492 (tmtt) REVERT: A 466 ILE cc_start: 0.9470 (mt) cc_final: 0.9260 (mt) REVERT: B 81 MET cc_start: 0.7752 (pmm) cc_final: 0.7284 (ppp) REVERT: B 232 TRP cc_start: 0.8866 (t-100) cc_final: 0.8260 (t-100) REVERT: B 281 GLU cc_start: 0.9367 (pm20) cc_final: 0.9165 (pp20) REVERT: B 329 CYS cc_start: 0.9325 (m) cc_final: 0.8925 (m) REVERT: B 333 LEU cc_start: 0.9411 (mm) cc_final: 0.8730 (tp) REVERT: B 347 PHE cc_start: 0.9398 (t80) cc_final: 0.9098 (t80) REVERT: B 444 LEU cc_start: 0.9106 (tt) cc_final: 0.8767 (tt) REVERT: B 458 LYS cc_start: 0.9696 (tmtt) cc_final: 0.9460 (tmtt) REVERT: B 484 ASP cc_start: 0.9634 (t70) cc_final: 0.9263 (t0) REVERT: B 487 ASP cc_start: 0.9592 (t0) cc_final: 0.9321 (p0) REVERT: C 81 MET cc_start: 0.7527 (pmm) cc_final: 0.7081 (ppp) REVERT: C 208 GLU cc_start: 0.9676 (pt0) cc_final: 0.9360 (pp20) REVERT: C 344 PHE cc_start: 0.9453 (t80) cc_final: 0.9133 (t80) REVERT: C 347 PHE cc_start: 0.9323 (t80) cc_final: 0.8845 (t80) REVERT: C 349 GLN cc_start: 0.9276 (tt0) cc_final: 0.8633 (tm-30) REVERT: C 353 LEU cc_start: 0.9584 (mt) cc_final: 0.8936 (mt) REVERT: C 458 LYS cc_start: 0.9768 (tmtt) cc_final: 0.9547 (tmtt) REVERT: C 460 ASP cc_start: 0.8997 (t70) cc_final: 0.8378 (t0) REVERT: C 469 LEU cc_start: 0.9113 (mt) cc_final: 0.8823 (mt) REVERT: D 81 MET cc_start: 0.7432 (pmm) cc_final: 0.7166 (ppp) REVERT: D 329 CYS cc_start: 0.9295 (m) cc_final: 0.8832 (m) REVERT: D 333 LEU cc_start: 0.9485 (mm) cc_final: 0.9004 (tp) REVERT: D 344 PHE cc_start: 0.9635 (t80) cc_final: 0.9406 (t80) REVERT: D 347 PHE cc_start: 0.9585 (t80) cc_final: 0.9205 (t80) REVERT: D 441 LYS cc_start: 0.9484 (ttmt) cc_final: 0.9189 (ttmt) REVERT: D 469 LEU cc_start: 0.9238 (mt) cc_final: 0.9022 (mt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2692 time to fit residues: 76.4102 Evaluate side-chains 148 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 166 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 152 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 50.0000 chunk 1 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051596 restraints weight = 68040.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053394 restraints weight = 47741.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054661 restraints weight = 35993.790| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13740 Z= 0.146 Angle : 0.697 7.008 18624 Z= 0.356 Chirality : 0.043 0.168 2000 Planarity : 0.005 0.046 2456 Dihedral : 5.241 28.283 1868 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.15 (0.20), residues: 1672 helix: 0.25 (0.18), residues: 800 sheet: -4.07 (0.55), residues: 56 loop : -3.10 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 165 HIS 0.007 0.001 HIS A 251 PHE 0.022 0.002 PHE A 255 TYR 0.011 0.001 TYR D 396 ARG 0.005 0.000 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 588) hydrogen bonds : angle 5.73466 ( 1728) covalent geometry : bond 0.00305 (13740) covalent geometry : angle 0.69717 (18624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.666 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 81 MET cc_start: 0.7954 (pmm) cc_final: 0.7621 (ppp) REVERT: A 303 LEU cc_start: 0.9321 (mm) cc_final: 0.9027 (mm) REVERT: A 331 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8387 (pt0) REVERT: A 441 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9190 (ttmt) REVERT: B 81 MET cc_start: 0.7557 (pmm) cc_final: 0.7187 (ppp) REVERT: B 232 TRP cc_start: 0.8775 (t-100) cc_final: 0.8194 (t-100) REVERT: B 329 CYS cc_start: 0.9414 (m) cc_final: 0.8890 (t) REVERT: B 333 LEU cc_start: 0.9418 (mm) cc_final: 0.8700 (tp) REVERT: B 347 PHE cc_start: 0.9437 (t80) cc_final: 0.9213 (t80) REVERT: B 388 TYR cc_start: 0.9089 (p90) cc_final: 0.8618 (p90) REVERT: B 441 LYS cc_start: 0.9558 (mtmm) cc_final: 0.9297 (mtpp) REVERT: B 484 ASP cc_start: 0.9499 (t70) cc_final: 0.9284 (t0) REVERT: B 487 ASP cc_start: 0.9538 (t0) cc_final: 0.9314 (p0) REVERT: C 81 MET cc_start: 0.7212 (pmm) cc_final: 0.6829 (ppp) REVERT: C 178 HIS cc_start: 0.9166 (m-70) cc_final: 0.8941 (m170) REVERT: C 208 GLU cc_start: 0.9655 (pt0) cc_final: 0.9333 (pp20) REVERT: C 347 PHE cc_start: 0.9353 (t80) cc_final: 0.8958 (t80) REVERT: C 349 GLN cc_start: 0.9293 (tt0) cc_final: 0.8510 (tm-30) REVERT: C 353 LEU cc_start: 0.9605 (mt) cc_final: 0.8967 (mt) REVERT: C 445 ARG cc_start: 0.9475 (mmt180) cc_final: 0.9148 (mtm110) REVERT: C 458 LYS cc_start: 0.9757 (tmtt) cc_final: 0.9510 (tmtt) REVERT: C 460 ASP cc_start: 0.9133 (t70) cc_final: 0.8473 (t0) REVERT: C 466 ILE cc_start: 0.9683 (mt) cc_final: 0.9277 (mt) REVERT: C 469 LEU cc_start: 0.9166 (mt) cc_final: 0.8872 (mt) REVERT: D 81 MET cc_start: 0.7349 (pmm) cc_final: 0.7122 (ppp) REVERT: D 232 TRP cc_start: 0.8480 (t-100) cc_final: 0.8223 (t-100) REVERT: D 329 CYS cc_start: 0.9185 (m) cc_final: 0.8801 (m) REVERT: D 333 LEU cc_start: 0.9541 (mm) cc_final: 0.9011 (tp) REVERT: D 347 PHE cc_start: 0.9528 (t80) cc_final: 0.8796 (t80) REVERT: D 441 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9068 (mtpt) REVERT: D 469 LEU cc_start: 0.9282 (mt) cc_final: 0.9079 (mt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2673 time to fit residues: 77.6394 Evaluate side-chains 150 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.0270 chunk 43 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 overall best weight: 4.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.050364 restraints weight = 69114.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052089 restraints weight = 48916.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053300 restraints weight = 37157.015| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.004 0.049 13740 Z= 0.178 Angle : 0.706 6.926 18624 Z= 0.363 Chirality : 0.044 0.193 2000 Planarity : 0.005 0.047 2456 Dihedral : 5.270 29.345 1868 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -2.17 (0.20), residues: 1672 helix: 0.24 (0.18), residues: 808 sheet: -4.08 (0.56), residues: 56 loop : -3.16 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 165 HIS 0.007 0.002 HIS C 177 PHE 0.027 0.002 PHE C 305 TYR 0.016 0.002 TYR A 313 ARG 0.011 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 588) hydrogen bonds : angle 5.87022 ( 1728) covalent geometry : bond 0.00367 (13740) covalent geometry : angle 0.70648 (18624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.539 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: symmetry clash REVERT: A 81 MET cc_start: 0.7918 (pmm) cc_final: 0.7609 (ppp) REVERT: A 303 LEU cc_start: 0.9316 (mm) cc_final: 0.8953 (mm) REVERT: A 331 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8462 (pt0) REVERT: A 441 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9199 (ttmt) REVERT: B 81 MET cc_start: 0.7567 (pmm) cc_final: 0.7213 (ppp) REVERT: B 232 TRP cc_start: 0.8825 (t-100) cc_final: 0.8204 (t-100) REVERT: B 329 CYS cc_start: 0.9406 (m) cc_final: 0.8902 (t) REVERT: B 333 LEU cc_start: 0.9380 (mm) cc_final: 0.8703 (tp) REVERT: B 347 PHE cc_start: 0.9475 (t80) cc_final: 0.9199 (t80) REVERT: B 444 LEU cc_start: 0.9104 (tt) cc_final: 0.8754 (tt) REVERT: B 484 ASP cc_start: 0.9490 (t70) cc_final: 0.9254 (t0) REVERT: B 487 ASP cc_start: 0.9568 (t0) cc_final: 0.9356 (p0) REVERT: C 81 MET cc_start: 0.7192 (pmm) cc_final: 0.6835 (ppp) REVERT: C 208 GLU cc_start: 0.9665 (pt0) cc_final: 0.9325 (pp20) REVERT: C 347 PHE cc_start: 0.9378 (t80) cc_final: 0.9161 (t80) REVERT: C 445 ARG cc_start: 0.9427 (mmt180) cc_final: 0.9116 (mtm110) REVERT: C 458 LYS cc_start: 0.9773 (tmtt) cc_final: 0.9519 (tmtt) REVERT: C 460 ASP cc_start: 0.9181 (t70) cc_final: 0.8579 (t0) REVERT: C 469 LEU cc_start: 0.9184 (mt) cc_final: 0.8881 (mt) REVERT: D 81 MET cc_start: 0.7480 (pmm) cc_final: 0.7271 (ppp) REVERT: D 232 TRP cc_start: 0.8578 (t-100) cc_final: 0.8202 (t-100) REVERT: D 329 CYS cc_start: 0.9249 (m) cc_final: 0.8849 (m) REVERT: D 333 LEU cc_start: 0.9576 (mm) cc_final: 0.9016 (tp) REVERT: D 347 PHE cc_start: 0.9515 (t80) cc_final: 0.8855 (t80) REVERT: D 441 LYS cc_start: 0.9438 (ttmt) cc_final: 0.9042 (mtpt) REVERT: D 466 ILE cc_start: 0.9532 (mt) cc_final: 0.9135 (mt) REVERT: D 469 LEU cc_start: 0.9244 (mt) cc_final: 0.9030 (mt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2958 time to fit residues: 84.6338 Evaluate side-chains 147 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.076448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049781 restraints weight = 69041.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051555 restraints weight = 49116.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052828 restraints weight = 36939.238| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13740 Z= 0.189 Angle : 0.726 7.648 18624 Z= 0.374 Chirality : 0.044 0.172 2000 Planarity : 0.005 0.058 2456 Dihedral : 5.345 28.640 1868 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -2.26 (0.20), residues: 1672 helix: 0.10 (0.18), residues: 828 sheet: -4.14 (0.57), residues: 56 loop : -3.19 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 165 HIS 0.008 0.002 HIS B 111 PHE 0.025 0.002 PHE A 255 TYR 0.012 0.002 TYR A 313 ARG 0.019 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 588) hydrogen bonds : angle 5.90928 ( 1728) covalent geometry : bond 0.00384 (13740) covalent geometry : angle 0.72596 (18624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.654 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 81 MET cc_start: 0.7943 (pmm) cc_final: 0.7613 (ppp) REVERT: A 303 LEU cc_start: 0.9281 (mm) cc_final: 0.8993 (mm) REVERT: A 331 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8508 (pt0) REVERT: A 347 PHE cc_start: 0.9640 (t80) cc_final: 0.9174 (t80) REVERT: A 441 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9142 (ttmt) REVERT: A 484 ASP cc_start: 0.9370 (t70) cc_final: 0.8905 (t0) REVERT: A 487 ASP cc_start: 0.9485 (t0) cc_final: 0.9158 (p0) REVERT: B 81 MET cc_start: 0.7533 (pmm) cc_final: 0.7178 (ppp) REVERT: B 232 TRP cc_start: 0.8837 (t-100) cc_final: 0.8214 (t-100) REVERT: B 329 CYS cc_start: 0.9451 (m) cc_final: 0.8994 (t) REVERT: B 444 LEU cc_start: 0.8990 (tt) cc_final: 0.8768 (tt) REVERT: B 484 ASP cc_start: 0.9563 (t70) cc_final: 0.9309 (t0) REVERT: B 487 ASP cc_start: 0.9569 (t0) cc_final: 0.9353 (p0) REVERT: C 81 MET cc_start: 0.7232 (pmm) cc_final: 0.6883 (ppp) REVERT: C 208 GLU cc_start: 0.9662 (pt0) cc_final: 0.9317 (pp20) REVERT: C 347 PHE cc_start: 0.9410 (t80) cc_final: 0.8791 (t80) REVERT: C 349 GLN cc_start: 0.9306 (tt0) cc_final: 0.8604 (tm-30) REVERT: C 353 LEU cc_start: 0.9560 (mt) cc_final: 0.8951 (mt) REVERT: C 444 LEU cc_start: 0.9009 (tt) cc_final: 0.8560 (tt) REVERT: C 458 LYS cc_start: 0.9690 (tmtt) cc_final: 0.9427 (tmtt) REVERT: C 460 ASP cc_start: 0.9186 (t70) cc_final: 0.8539 (t0) REVERT: C 469 LEU cc_start: 0.9072 (mt) cc_final: 0.8733 (mt) REVERT: D 81 MET cc_start: 0.7510 (pmm) cc_final: 0.7305 (ppp) REVERT: D 232 TRP cc_start: 0.8576 (t-100) cc_final: 0.8271 (t-100) REVERT: D 280 LYS cc_start: 0.9392 (ptpt) cc_final: 0.9183 (pttm) REVERT: D 281 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9144 (mt-10) REVERT: D 329 CYS cc_start: 0.9279 (m) cc_final: 0.8851 (m) REVERT: D 333 LEU cc_start: 0.9589 (mm) cc_final: 0.8994 (tp) REVERT: D 347 PHE cc_start: 0.9546 (t80) cc_final: 0.8967 (t80) REVERT: D 441 LYS cc_start: 0.9468 (ttmt) cc_final: 0.9091 (mtpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2624 time to fit residues: 74.4343 Evaluate side-chains 139 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.074695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048826 restraints weight = 70401.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050466 restraints weight = 49952.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051636 restraints weight = 37898.888| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13740 Z= 0.244 Angle : 0.776 8.758 18624 Z= 0.402 Chirality : 0.045 0.180 2000 Planarity : 0.006 0.072 2456 Dihedral : 5.503 29.426 1868 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -2.41 (0.20), residues: 1672 helix: -0.08 (0.18), residues: 828 sheet: -4.38 (0.51), residues: 56 loop : -3.20 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 165 HIS 0.008 0.002 HIS C 178 PHE 0.041 0.002 PHE A 285 TYR 0.015 0.002 TYR A 313 ARG 0.015 0.001 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 588) hydrogen bonds : angle 6.09353 ( 1728) covalent geometry : bond 0.00480 (13740) covalent geometry : angle 0.77569 (18624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.687 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 81 MET cc_start: 0.7929 (pmm) cc_final: 0.7596 (ppp) REVERT: A 178 HIS cc_start: 0.9151 (m90) cc_final: 0.8930 (m90) REVERT: A 255 PHE cc_start: 0.9097 (t80) cc_final: 0.8890 (t80) REVERT: A 331 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8607 (pt0) REVERT: A 338 MET cc_start: 0.8933 (mmp) cc_final: 0.8717 (mmp) REVERT: A 347 PHE cc_start: 0.9557 (t80) cc_final: 0.9141 (t80) REVERT: A 399 LEU cc_start: 0.9610 (tt) cc_final: 0.9200 (tp) REVERT: A 441 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9145 (ttmt) REVERT: A 484 ASP cc_start: 0.9400 (t70) cc_final: 0.9005 (t0) REVERT: A 487 ASP cc_start: 0.9534 (t0) cc_final: 0.9152 (p0) REVERT: B 81 MET cc_start: 0.7600 (pmm) cc_final: 0.7234 (ppp) REVERT: B 232 TRP cc_start: 0.8795 (t-100) cc_final: 0.8188 (t-100) REVERT: B 484 ASP cc_start: 0.9668 (t70) cc_final: 0.9291 (t0) REVERT: B 487 ASP cc_start: 0.9605 (t0) cc_final: 0.9349 (p0) REVERT: C 81 MET cc_start: 0.7257 (pmm) cc_final: 0.6895 (ppp) REVERT: C 202 ARG cc_start: 0.9792 (mtt180) cc_final: 0.9084 (ptp-110) REVERT: C 208 GLU cc_start: 0.9673 (pt0) cc_final: 0.9330 (pp20) REVERT: C 347 PHE cc_start: 0.9418 (t80) cc_final: 0.8809 (t80) REVERT: C 444 LEU cc_start: 0.8829 (tt) cc_final: 0.8265 (tt) REVERT: C 458 LYS cc_start: 0.9639 (tmtt) cc_final: 0.9348 (tmtt) REVERT: C 460 ASP cc_start: 0.9135 (t70) cc_final: 0.8484 (t0) REVERT: C 469 LEU cc_start: 0.9173 (mt) cc_final: 0.8883 (mt) REVERT: D 81 MET cc_start: 0.7529 (pmm) cc_final: 0.7326 (ppp) REVERT: D 232 TRP cc_start: 0.8611 (t-100) cc_final: 0.8286 (t-100) REVERT: D 347 PHE cc_start: 0.9534 (t80) cc_final: 0.8928 (t80) REVERT: D 441 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9083 (mtpt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2717 time to fit residues: 75.0684 Evaluate side-chains 142 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.077383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051805 restraints weight = 66777.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053624 restraints weight = 46381.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054998 restraints weight = 34597.288| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13740 Z= 0.154 Angle : 0.720 7.776 18624 Z= 0.370 Chirality : 0.044 0.184 2000 Planarity : 0.005 0.049 2456 Dihedral : 5.256 27.245 1868 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.20), residues: 1672 helix: 0.19 (0.18), residues: 804 sheet: -4.22 (0.52), residues: 56 loop : -3.00 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 165 HIS 0.006 0.001 HIS D 251 PHE 0.028 0.002 PHE A 255 TYR 0.011 0.001 TYR D 264 ARG 0.014 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 588) hydrogen bonds : angle 5.82010 ( 1728) covalent geometry : bond 0.00325 (13740) covalent geometry : angle 0.72026 (18624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4379.56 seconds wall clock time: 77 minutes 46.68 seconds (4666.68 seconds total)