Starting phenix.real_space_refine on Wed Mar 4 11:22:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a2g_11624/03_2026/7a2g_11624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a2g_11624/03_2026/7a2g_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_11624/03_2026/7a2g_11624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a2g_11624/03_2026/7a2g_11624.map" model { file = "/net/cci-nas-00/data/ceres_data/7a2g_11624/03_2026/7a2g_11624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a2g_11624/03_2026/7a2g_11624.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.10, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 445.2 milliseconds 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: 0.39 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: 1.89 Time building geometry restraints manager: 1.42 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: 0.01 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- 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 : 47.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG C 138 TYR 0.020 0.002 TYR A 243 PHE 0.024 0.002 PHE D 194 TRP 0.020 0.003 TRP B 165 HIS 0.018 0.003 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00569 (13740) covalent geometry : angle 0.85757 (18624) hydrogen bonds : bond 0.21519 ( 588) hydrogen bonds : angle 7.90519 ( 1728) *********************** 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 : 0.517 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: 0.8940 (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: 0.1315 time to fit residues: 39.1539 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 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 309 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048417 restraints weight = 65194.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050067 restraints weight = 47230.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051278 restraints weight = 35420.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052110 restraints weight = 28775.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052740 restraints weight = 24433.775| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13740 Z= 0.194 Angle : 0.771 7.916 18624 Z= 0.401 Chirality : 0.044 0.171 2000 Planarity : 0.006 0.046 2456 Dihedral : 5.891 31.204 1868 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 0.35 % Allowed : 8.19 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.18), residues: 1672 helix: -1.23 (0.16), residues: 796 sheet: -4.48 (0.35), residues: 104 loop : -3.95 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 288 TYR 0.016 0.002 TYR B 213 PHE 0.020 0.002 PHE C 347 TRP 0.014 0.002 TRP B 165 HIS 0.013 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00390 (13740) covalent geometry : angle 0.77114 (18624) hydrogen bonds : bond 0.06402 ( 588) hydrogen bonds : angle 6.42081 ( 1728) *********************** 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 224 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.442 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: A 81 MET cc_start: 0.7689 (pmm) cc_final: 0.7412 (ppp) REVERT: A 166 PHE cc_start: 0.9508 (p90) cc_final: 0.9166 (p90) REVERT: A 208 GLU cc_start: 0.9557 (pt0) cc_final: 0.9149 (pp20) REVERT: A 277 ARG cc_start: 0.9396 (ttm170) cc_final: 0.9070 (mtt180) REVERT: A 281 GLU cc_start: 0.9770 (mm-30) cc_final: 0.9460 (mm-30) REVERT: A 303 LEU cc_start: 0.9357 (mm) cc_final: 0.9078 (mm) REVERT: A 445 ARG cc_start: 0.9645 (ptt90) cc_final: 0.9424 (ptt90) REVERT: B 81 MET cc_start: 0.7293 (pmm) cc_final: 0.6945 (ppp) REVERT: B 344 PHE cc_start: 0.9306 (t80) cc_final: 0.8684 (t80) REVERT: B 347 PHE cc_start: 0.9191 (t80) cc_final: 0.8893 (t80) REVERT: B 349 GLN cc_start: 0.9535 (tt0) cc_final: 0.9316 (tt0) REVERT: B 388 TYR cc_start: 0.9042 (p90) cc_final: 0.8523 (p90) REVERT: B 441 LYS cc_start: 0.9517 (mtmm) cc_final: 0.9269 (mttt) REVERT: B 487 ASP cc_start: 0.9540 (t0) cc_final: 0.9302 (p0) REVERT: C 81 MET cc_start: 0.7435 (pmm) cc_final: 0.7023 (ppp) REVERT: C 208 GLU cc_start: 0.9624 (pt0) cc_final: 0.9261 (pp20) REVERT: C 303 LEU cc_start: 0.9509 (mm) cc_final: 0.9195 (mm) REVERT: C 388 TYR cc_start: 0.8871 (p90) cc_final: 0.8622 (p90) REVERT: C 458 LYS cc_start: 0.9588 (tmtt) cc_final: 0.9299 (tmtt) REVERT: C 467 ASP cc_start: 0.9052 (m-30) cc_final: 0.7137 (m-30) REVERT: D 81 MET cc_start: 0.7524 (pmm) cc_final: 0.7184 (ppp) REVERT: D 173 LEU cc_start: 0.9764 (mm) cc_final: 0.9537 (mm) REVERT: D 344 PHE cc_start: 0.9531 (t80) cc_final: 0.9086 (t80) REVERT: D 347 PHE cc_start: 0.9615 (t80) cc_final: 0.8998 (t80) REVERT: D 441 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9026 (ttmt) outliers start: 5 outliers final: 1 residues processed: 224 average time/residue: 0.1308 time to fit residues: 41.2689 Evaluate side-chains 168 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 50 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 0.1980 chunk 134 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 133 optimal weight: 30.0000 overall best weight: 3.8392 ------------------------------------------------------------------------------- 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 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** 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 381 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 = 0.3613 r_free = 0.3613 target = 0.076132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050607 restraints weight = 66644.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052298 restraints weight = 47229.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053499 restraints weight = 35781.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054402 restraints weight = 28690.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055126 restraints weight = 24268.903| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13740 Z= 0.179 Angle : 0.733 7.316 18624 Z= 0.380 Chirality : 0.044 0.200 2000 Planarity : 0.006 0.082 2456 Dihedral : 5.639 30.487 1868 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.19), residues: 1672 helix: -0.54 (0.17), residues: 796 sheet: -4.50 (0.35), residues: 104 loop : -3.61 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 288 TYR 0.042 0.002 TYR A 243 PHE 0.024 0.002 PHE C 347 TRP 0.027 0.002 TRP A 165 HIS 0.028 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00363 (13740) covalent geometry : angle 0.73271 (18624) hydrogen bonds : bond 0.05512 ( 588) hydrogen bonds : angle 6.11668 ( 1728) *********************** 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 211 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.530 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: symmetry clash REVERT: A 81 MET cc_start: 0.7963 (pmm) cc_final: 0.7564 (ppp) REVERT: A 168 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8620 (mmm-85) REVERT: A 178 HIS cc_start: 0.8989 (m-70) cc_final: 0.8780 (m-70) REVERT: A 208 GLU cc_start: 0.9552 (pt0) cc_final: 0.9151 (pp20) REVERT: A 277 ARG cc_start: 0.9398 (ttm170) cc_final: 0.9030 (mmt180) REVERT: A 281 GLU cc_start: 0.9783 (mm-30) cc_final: 0.9459 (mm-30) REVERT: A 303 LEU cc_start: 0.9361 (mm) cc_final: 0.9076 (mm) REVERT: A 331 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8518 (pt0) REVERT: A 441 LYS cc_start: 0.9479 (tttp) cc_final: 0.8950 (mmtt) REVERT: A 445 ARG cc_start: 0.9631 (ptt90) cc_final: 0.9409 (ptt90) REVERT: B 81 MET cc_start: 0.7513 (pmm) cc_final: 0.6985 (ppp) REVERT: B 331 GLU cc_start: 0.8451 (pt0) cc_final: 0.8240 (pt0) REVERT: B 344 PHE cc_start: 0.9365 (t80) cc_final: 0.8954 (t80) REVERT: B 347 PHE cc_start: 0.9246 (t80) cc_final: 0.9020 (t80) REVERT: B 441 LYS cc_start: 0.9513 (mtmm) cc_final: 0.9227 (mttt) REVERT: B 484 ASP cc_start: 0.9653 (t70) cc_final: 0.9283 (t0) REVERT: B 487 ASP cc_start: 0.9561 (t0) cc_final: 0.9309 (p0) REVERT: C 81 MET cc_start: 0.7450 (pmm) cc_final: 0.7071 (ppp) REVERT: C 202 ARG cc_start: 0.9625 (mtp180) cc_final: 0.9408 (mtt-85) REVERT: C 208 GLU cc_start: 0.9658 (pt0) cc_final: 0.9342 (pp20) REVERT: C 388 TYR cc_start: 0.8873 (p90) cc_final: 0.8644 (p90) REVERT: C 458 LYS cc_start: 0.9621 (tmtt) cc_final: 0.9372 (tmtt) REVERT: D 81 MET cc_start: 0.7331 (pmm) cc_final: 0.7071 (ppp) REVERT: D 277 ARG cc_start: 0.9487 (mtt90) cc_final: 0.9210 (mmt180) REVERT: D 329 CYS cc_start: 0.9249 (m) cc_final: 0.8788 (m) REVERT: D 333 LEU cc_start: 0.9458 (mm) cc_final: 0.8612 (tp) REVERT: D 344 PHE cc_start: 0.9520 (t80) cc_final: 0.9103 (t80) REVERT: D 347 PHE cc_start: 0.9552 (t80) cc_final: 0.8962 (t80) REVERT: D 441 LYS cc_start: 0.9470 (ttmt) cc_final: 0.9129 (ttmt) REVERT: D 444 LEU cc_start: 0.9446 (tt) cc_final: 0.9052 (tt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1303 time to fit residues: 38.7217 Evaluate side-chains 158 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 129 optimal weight: 30.0000 chunk 150 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 98 optimal weight: 0.0010 chunk 96 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.9592 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.074695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049181 restraints weight = 68177.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050840 restraints weight = 48443.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051822 restraints weight = 36930.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052852 restraints weight = 30456.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053521 restraints weight = 25784.345| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13740 Z= 0.195 Angle : 0.725 7.391 18624 Z= 0.375 Chirality : 0.044 0.204 2000 Planarity : 0.005 0.058 2456 Dihedral : 5.560 30.725 1868 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.19), residues: 1672 helix: -0.27 (0.17), residues: 804 sheet: -4.46 (0.35), residues: 104 loop : -3.42 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.025 0.002 TYR A 243 PHE 0.021 0.002 PHE C 347 TRP 0.024 0.002 TRP A 165 HIS 0.018 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00392 (13740) covalent geometry : angle 0.72494 (18624) hydrogen bonds : bond 0.05173 ( 588) hydrogen bonds : angle 5.98373 ( 1728) *********************** 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 204 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.487 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: 0.8000 (pmm) cc_final: 0.7635 (ppp) REVERT: A 178 HIS cc_start: 0.9082 (m-70) cc_final: 0.8868 (m-70) REVERT: A 208 GLU cc_start: 0.9547 (pt0) cc_final: 0.9151 (pp20) REVERT: A 303 LEU cc_start: 0.9378 (mm) cc_final: 0.9063 (mm) REVERT: A 331 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8535 (pt0) REVERT: A 441 LYS cc_start: 0.9519 (ttmm) cc_final: 0.9093 (mtpt) REVERT: A 458 LYS cc_start: 0.9576 (tmtt) cc_final: 0.9304 (tmtt) REVERT: A 467 ASP cc_start: 0.9008 (m-30) cc_final: 0.8212 (m-30) REVERT: B 81 MET cc_start: 0.7542 (pmm) cc_final: 0.7022 (ppp) REVERT: B 347 PHE cc_start: 0.9298 (t80) cc_final: 0.9061 (t80) REVERT: B 441 LYS cc_start: 0.9505 (mtmm) cc_final: 0.9215 (mttt) REVERT: B 444 LEU cc_start: 0.9289 (tt) cc_final: 0.9034 (tt) REVERT: B 458 LYS cc_start: 0.9711 (tmtt) cc_final: 0.9457 (tmtt) REVERT: B 484 ASP cc_start: 0.9636 (t70) cc_final: 0.9344 (t0) REVERT: B 487 ASP cc_start: 0.9560 (t0) cc_final: 0.9313 (p0) REVERT: C 81 MET cc_start: 0.7506 (pmm) cc_final: 0.7119 (ppp) REVERT: C 208 GLU cc_start: 0.9682 (pt0) cc_final: 0.9369 (pp20) REVERT: C 344 PHE cc_start: 0.9412 (t80) cc_final: 0.8997 (t80) REVERT: C 347 PHE cc_start: 0.9312 (t80) cc_final: 0.8901 (t80) REVERT: C 444 LEU cc_start: 0.9060 (tt) cc_final: 0.8810 (tt) REVERT: C 458 LYS cc_start: 0.9675 (tmtt) cc_final: 0.9416 (tmtt) REVERT: C 469 LEU cc_start: 0.8998 (mt) cc_final: 0.8647 (mt) REVERT: D 81 MET cc_start: 0.7465 (pmm) cc_final: 0.7209 (ppp) REVERT: D 232 TRP cc_start: 0.8542 (t-100) cc_final: 0.8305 (t-100) REVERT: D 344 PHE cc_start: 0.9595 (t80) cc_final: 0.9147 (t80) REVERT: D 347 PHE cc_start: 0.9562 (t80) cc_final: 0.8929 (t80) REVERT: D 441 LYS cc_start: 0.9493 (ttmt) cc_final: 0.9185 (ttmt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1232 time to fit residues: 35.5513 Evaluate side-chains 154 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 111 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 130 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 122 optimal weight: 0.0470 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.077193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051689 restraints weight = 66136.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053451 restraints weight = 46494.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054692 restraints weight = 34970.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055731 restraints weight = 27970.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.056544 restraints weight = 23202.692| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13740 Z= 0.151 Angle : 0.715 8.476 18624 Z= 0.364 Chirality : 0.044 0.196 2000 Planarity : 0.005 0.073 2456 Dihedral : 5.431 29.010 1868 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.20), residues: 1672 helix: 0.02 (0.18), residues: 796 sheet: -4.34 (0.37), residues: 104 loop : -3.29 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 288 TYR 0.021 0.002 TYR A 243 PHE 0.033 0.002 PHE A 305 TRP 0.015 0.002 TRP A 165 HIS 0.012 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00317 (13740) covalent geometry : angle 0.71482 (18624) hydrogen bonds : bond 0.04882 ( 588) hydrogen bonds : angle 5.81149 ( 1728) *********************** 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 216 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.426 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: symmetry clash REVERT: A 81 MET cc_start: 0.7981 (pmm) cc_final: 0.7603 (ppp) REVERT: A 208 GLU cc_start: 0.9524 (pt0) cc_final: 0.9110 (pp20) REVERT: A 303 LEU cc_start: 0.9247 (mm) cc_final: 0.8959 (mm) REVERT: A 331 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8385 (pt0) REVERT: A 441 LYS cc_start: 0.9508 (ttmm) cc_final: 0.8991 (mtpt) REVERT: A 458 LYS cc_start: 0.9547 (tmtt) cc_final: 0.9225 (tmtt) REVERT: A 467 ASP cc_start: 0.8916 (m-30) cc_final: 0.7906 (m-30) REVERT: B 81 MET cc_start: 0.7490 (pmm) cc_final: 0.6986 (ppp) REVERT: B 232 TRP cc_start: 0.8852 (t-100) cc_final: 0.8448 (t-100) REVERT: B 329 CYS cc_start: 0.9386 (m) cc_final: 0.8906 (t) REVERT: B 441 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9170 (mttt) REVERT: B 484 ASP cc_start: 0.9593 (t70) cc_final: 0.9358 (t0) REVERT: B 487 ASP cc_start: 0.9561 (t0) cc_final: 0.9298 (p0) REVERT: C 81 MET cc_start: 0.7465 (pmm) cc_final: 0.7073 (ppp) REVERT: C 208 GLU cc_start: 0.9660 (pt0) cc_final: 0.9328 (pp20) REVERT: C 344 PHE cc_start: 0.9425 (t80) cc_final: 0.9159 (t80) REVERT: C 347 PHE cc_start: 0.9253 (t80) cc_final: 0.8827 (t80) REVERT: C 458 LYS cc_start: 0.9695 (tmtt) cc_final: 0.9448 (tmtt) REVERT: C 460 ASP cc_start: 0.8901 (t70) cc_final: 0.8272 (t0) REVERT: C 469 LEU cc_start: 0.9039 (mt) cc_final: 0.8720 (mt) REVERT: D 81 MET cc_start: 0.7460 (pmm) cc_final: 0.7200 (ppp) REVERT: D 232 TRP cc_start: 0.8552 (t-100) cc_final: 0.8320 (t-100) REVERT: D 329 CYS cc_start: 0.9222 (m) cc_final: 0.8835 (m) REVERT: D 333 LEU cc_start: 0.9539 (mm) cc_final: 0.8978 (tp) REVERT: D 344 PHE cc_start: 0.9624 (t80) cc_final: 0.9194 (t80) REVERT: D 347 PHE cc_start: 0.9540 (t80) cc_final: 0.8826 (t80) REVERT: D 441 LYS cc_start: 0.9489 (ttmt) cc_final: 0.9097 (mtpt) REVERT: D 469 LEU cc_start: 0.9370 (mt) cc_final: 0.9063 (mt) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1229 time to fit residues: 37.4714 Evaluate side-chains 159 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 10.0000 chunk 42 optimal weight: 50.0000 chunk 101 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- 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 428 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** ** 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 = 0.3599 r_free = 0.3599 target = 0.074522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049467 restraints weight = 69644.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051111 restraints weight = 50089.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052333 restraints weight = 38096.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.053112 restraints weight = 30854.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053893 restraints weight = 26483.502| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13740 Z= 0.242 Angle : 0.769 7.218 18624 Z= 0.402 Chirality : 0.045 0.171 2000 Planarity : 0.006 0.051 2456 Dihedral : 5.660 31.079 1868 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 28.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.20), residues: 1672 helix: -0.25 (0.18), residues: 824 sheet: -4.64 (0.45), residues: 56 loop : -3.43 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 342 TYR 0.014 0.002 TYR D 213 PHE 0.022 0.002 PHE A 285 TRP 0.020 0.002 TRP B 165 HIS 0.009 0.002 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00475 (13740) covalent geometry : angle 0.76922 (18624) hydrogen bonds : bond 0.05198 ( 588) hydrogen bonds : angle 6.18219 ( 1728) *********************** 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 200 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.427 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: A 81 MET cc_start: 0.8013 (pmm) cc_final: 0.7626 (ppp) REVERT: A 303 LEU cc_start: 0.9294 (mm) cc_final: 0.8957 (mm) REVERT: A 331 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8561 (pt0) REVERT: A 347 PHE cc_start: 0.9523 (t80) cc_final: 0.9099 (t80) REVERT: A 441 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9009 (mtpt) REVERT: B 81 MET cc_start: 0.7630 (pmm) cc_final: 0.7163 (ppp) REVERT: B 232 TRP cc_start: 0.8885 (t-100) cc_final: 0.8262 (t-100) REVERT: B 281 GLU cc_start: 0.9626 (mp0) cc_final: 0.9374 (pp20) REVERT: B 329 CYS cc_start: 0.9349 (m) cc_final: 0.8923 (m) REVERT: B 333 LEU cc_start: 0.9360 (mm) cc_final: 0.8650 (tp) REVERT: B 338 MET cc_start: 0.8865 (mmp) cc_final: 0.8605 (mmp) REVERT: B 347 PHE cc_start: 0.9415 (t80) cc_final: 0.9106 (t80) REVERT: B 444 LEU cc_start: 0.9331 (tt) cc_final: 0.9076 (tt) REVERT: B 458 LYS cc_start: 0.9697 (tmtt) cc_final: 0.9464 (tmtt) REVERT: B 484 ASP cc_start: 0.9646 (t70) cc_final: 0.9287 (t0) REVERT: B 487 ASP cc_start: 0.9588 (t0) cc_final: 0.9312 (p0) REVERT: C 81 MET cc_start: 0.7508 (pmm) cc_final: 0.7099 (ppp) REVERT: C 208 GLU cc_start: 0.9674 (pt0) cc_final: 0.9354 (pp20) REVERT: C 344 PHE cc_start: 0.9462 (t80) cc_final: 0.9181 (t80) REVERT: C 347 PHE cc_start: 0.9324 (t80) cc_final: 0.8877 (t80) REVERT: C 349 GLN cc_start: 0.9265 (tt0) cc_final: 0.8624 (tm-30) REVERT: C 353 LEU cc_start: 0.9551 (mt) cc_final: 0.8866 (mt) REVERT: C 469 LEU cc_start: 0.9085 (mt) cc_final: 0.8802 (mt) REVERT: D 81 MET cc_start: 0.7495 (pmm) cc_final: 0.7233 (ppp) REVERT: D 168 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8883 (mmm-85) REVERT: D 281 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9101 (mt-10) REVERT: D 321 MET cc_start: 0.9164 (tpt) cc_final: 0.8905 (tpt) REVERT: D 329 CYS cc_start: 0.9272 (m) cc_final: 0.8853 (m) REVERT: D 333 LEU cc_start: 0.9533 (mm) cc_final: 0.9055 (tp) REVERT: D 344 PHE cc_start: 0.9617 (t80) cc_final: 0.9018 (t80) REVERT: D 347 PHE cc_start: 0.9540 (t80) cc_final: 0.8938 (t80) REVERT: D 441 LYS cc_start: 0.9490 (ttmt) cc_final: 0.9097 (mtpt) REVERT: D 466 ILE cc_start: 0.9612 (mt) cc_final: 0.9399 (mt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1199 time to fit residues: 34.6100 Evaluate side-chains 146 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** ** D 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** ** 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 = 0.3615 r_free = 0.3615 target = 0.075407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049895 restraints weight = 68743.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051596 restraints weight = 49071.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052401 restraints weight = 37077.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053598 restraints weight = 31300.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054385 restraints weight = 26135.913| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13740 Z= 0.201 Angle : 0.734 7.340 18624 Z= 0.380 Chirality : 0.044 0.180 2000 Planarity : 0.005 0.077 2456 Dihedral : 5.511 29.301 1868 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.20), residues: 1672 helix: -0.08 (0.18), residues: 800 sheet: -4.54 (0.47), residues: 56 loop : -3.25 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 168 TYR 0.015 0.002 TYR A 243 PHE 0.024 0.002 PHE B 344 TRP 0.014 0.002 TRP B 165 HIS 0.007 0.002 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00402 (13740) covalent geometry : angle 0.73383 (18624) hydrogen bonds : bond 0.04972 ( 588) hydrogen bonds : angle 5.99461 ( 1728) *********************** 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 198 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.428 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: A 81 MET cc_start: 0.7994 (pmm) cc_final: 0.7616 (ppp) REVERT: A 303 LEU cc_start: 0.9316 (mm) cc_final: 0.8977 (mm) REVERT: A 331 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8452 (pt0) REVERT: A 441 LYS cc_start: 0.9486 (ttmm) cc_final: 0.9201 (ttmt) REVERT: A 484 ASP cc_start: 0.9417 (t70) cc_final: 0.9151 (t0) REVERT: B 81 MET cc_start: 0.7614 (pmm) cc_final: 0.7183 (ppp) REVERT: B 232 TRP cc_start: 0.8843 (t-100) cc_final: 0.8259 (t-100) REVERT: B 329 CYS cc_start: 0.9370 (m) cc_final: 0.8978 (m) REVERT: B 333 LEU cc_start: 0.9377 (mm) cc_final: 0.8666 (tp) REVERT: B 338 MET cc_start: 0.8786 (mmp) cc_final: 0.8561 (mmp) REVERT: B 347 PHE cc_start: 0.9412 (t80) cc_final: 0.9136 (t80) REVERT: B 444 LEU cc_start: 0.9105 (tt) cc_final: 0.8880 (tt) REVERT: B 484 ASP cc_start: 0.9612 (t70) cc_final: 0.9235 (t0) REVERT: B 487 ASP cc_start: 0.9572 (t0) cc_final: 0.9310 (p0) REVERT: C 81 MET cc_start: 0.7362 (pmm) cc_final: 0.6931 (ppp) REVERT: C 208 GLU cc_start: 0.9648 (pt0) cc_final: 0.9319 (pp20) REVERT: C 349 GLN cc_start: 0.9212 (tt0) cc_final: 0.8568 (tm-30) REVERT: C 353 LEU cc_start: 0.9541 (mt) cc_final: 0.8919 (mt) REVERT: C 444 LEU cc_start: 0.9311 (tp) cc_final: 0.9086 (tt) REVERT: C 469 LEU cc_start: 0.9149 (mt) cc_final: 0.8882 (mt) REVERT: D 81 MET cc_start: 0.7503 (pmm) cc_final: 0.7235 (ppp) REVERT: D 281 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9125 (mt-10) REVERT: D 329 CYS cc_start: 0.9280 (m) cc_final: 0.8891 (m) REVERT: D 333 LEU cc_start: 0.9553 (mm) cc_final: 0.9100 (tp) REVERT: D 344 PHE cc_start: 0.9611 (t80) cc_final: 0.8937 (t80) REVERT: D 347 PHE cc_start: 0.9531 (t80) cc_final: 0.8690 (t80) REVERT: D 441 LYS cc_start: 0.9482 (ttmt) cc_final: 0.9062 (mtpt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1089 time to fit residues: 31.6301 Evaluate side-chains 141 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 0.0770 chunk 164 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.3645 r_free = 0.3645 target = 0.077403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051461 restraints weight = 65388.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053196 restraints weight = 46472.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054393 restraints weight = 35092.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.055249 restraints weight = 28218.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056046 restraints weight = 24020.065| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13740 Z= 0.152 Angle : 0.719 7.771 18624 Z= 0.369 Chirality : 0.044 0.169 2000 Planarity : 0.005 0.047 2456 Dihedral : 5.376 29.069 1868 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.20), residues: 1672 helix: 0.15 (0.18), residues: 804 sheet: -4.42 (0.49), residues: 56 loop : -3.17 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.048 0.002 TYR A 243 PHE 0.022 0.002 PHE B 305 TRP 0.013 0.002 TRP B 165 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00319 (13740) covalent geometry : angle 0.71874 (18624) hydrogen bonds : bond 0.04595 ( 588) hydrogen bonds : angle 5.78625 ( 1728) *********************** 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 195 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.516 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: 0.7957 (pmm) cc_final: 0.7593 (ppp) REVERT: A 169 LYS cc_start: 0.9017 (mppt) cc_final: 0.8728 (mppt) REVERT: A 331 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8375 (pt0) REVERT: A 347 PHE cc_start: 0.9590 (t80) cc_final: 0.9302 (t80) REVERT: A 441 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9226 (ttmt) REVERT: A 484 ASP cc_start: 0.9413 (t70) cc_final: 0.9207 (t0) REVERT: B 81 MET cc_start: 0.7528 (pmm) cc_final: 0.7148 (ppp) REVERT: B 178 HIS cc_start: 0.9330 (m-70) cc_final: 0.9108 (m90) REVERT: B 232 TRP cc_start: 0.8874 (t-100) cc_final: 0.8212 (t-100) REVERT: B 329 CYS cc_start: 0.9400 (m) cc_final: 0.8869 (t) REVERT: B 333 LEU cc_start: 0.9368 (mm) cc_final: 0.8677 (tp) REVERT: B 484 ASP cc_start: 0.9544 (t70) cc_final: 0.9260 (t0) REVERT: B 487 ASP cc_start: 0.9573 (t0) cc_final: 0.9327 (p0) REVERT: C 81 MET cc_start: 0.7276 (pmm) cc_final: 0.6851 (ppp) REVERT: C 178 HIS cc_start: 0.9151 (m-70) cc_final: 0.8905 (m170) REVERT: C 208 GLU cc_start: 0.9646 (pt0) cc_final: 0.9306 (pp20) REVERT: C 466 ILE cc_start: 0.9418 (mt) cc_final: 0.9160 (mt) REVERT: C 469 LEU cc_start: 0.9202 (mt) cc_final: 0.8926 (mt) REVERT: D 81 MET cc_start: 0.7320 (pmm) cc_final: 0.7064 (ppp) REVERT: D 168 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8782 (mmm-85) REVERT: D 329 CYS cc_start: 0.9255 (m) cc_final: 0.8846 (m) REVERT: D 333 LEU cc_start: 0.9584 (mm) cc_final: 0.9156 (tp) REVERT: D 344 PHE cc_start: 0.9417 (t80) cc_final: 0.9024 (t80) REVERT: D 347 PHE cc_start: 0.9446 (t80) cc_final: 0.9005 (t80) REVERT: D 441 LYS cc_start: 0.9538 (ttmt) cc_final: 0.9204 (ttmt) REVERT: D 466 ILE cc_start: 0.9502 (mt) cc_final: 0.9195 (mt) REVERT: D 469 LEU cc_start: 0.9304 (mt) cc_final: 0.9073 (mt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1153 time to fit residues: 32.4984 Evaluate side-chains 145 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 134 optimal weight: 0.0170 chunk 57 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- 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 ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050262 restraints weight = 67312.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051971 restraints weight = 47744.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053241 restraints weight = 35759.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054137 restraints weight = 28843.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054896 restraints weight = 24340.727| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13740 Z= 0.208 Angle : 0.748 9.507 18624 Z= 0.388 Chirality : 0.045 0.193 2000 Planarity : 0.005 0.051 2456 Dihedral : 5.437 29.088 1868 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.07 % Allowed : 0.70 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.20), residues: 1672 helix: -0.05 (0.18), residues: 824 sheet: -4.12 (0.45), residues: 96 loop : -3.10 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 277 TYR 0.013 0.002 TYR A 243 PHE 0.028 0.002 PHE B 305 TRP 0.019 0.002 TRP B 165 HIS 0.007 0.002 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00417 (13740) covalent geometry : angle 0.74837 (18624) hydrogen bonds : bond 0.04872 ( 588) hydrogen bonds : angle 5.99915 ( 1728) *********************** 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 194 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.403 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: A 81 MET cc_start: 0.8039 (pmm) cc_final: 0.7646 (ppp) REVERT: A 169 LYS cc_start: 0.8957 (mppt) cc_final: 0.8671 (mppt) REVERT: A 331 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8389 (pt0) REVERT: A 347 PHE cc_start: 0.9605 (t80) cc_final: 0.9357 (t80) REVERT: A 441 LYS cc_start: 0.9382 (ttmm) cc_final: 0.9138 (ttmt) REVERT: A 484 ASP cc_start: 0.9434 (t70) cc_final: 0.8934 (t0) REVERT: A 487 ASP cc_start: 0.9510 (t0) cc_final: 0.9153 (p0) REVERT: B 81 MET cc_start: 0.7628 (pmm) cc_final: 0.7211 (ppp) REVERT: B 178 HIS cc_start: 0.9365 (m-70) cc_final: 0.9073 (m-70) REVERT: B 232 TRP cc_start: 0.8856 (t-100) cc_final: 0.8231 (t-100) REVERT: B 281 GLU cc_start: 0.9645 (mp0) cc_final: 0.9334 (pp20) REVERT: B 444 LEU cc_start: 0.9212 (tt) cc_final: 0.8942 (tt) REVERT: B 484 ASP cc_start: 0.9613 (t70) cc_final: 0.9249 (t0) REVERT: B 487 ASP cc_start: 0.9679 (t0) cc_final: 0.9367 (p0) REVERT: C 81 MET cc_start: 0.7373 (pmm) cc_final: 0.6922 (ppp) REVERT: C 178 HIS cc_start: 0.9179 (m-70) cc_final: 0.8919 (m170) REVERT: C 208 GLU cc_start: 0.9654 (pt0) cc_final: 0.9297 (pp20) REVERT: C 347 PHE cc_start: 0.9470 (t80) cc_final: 0.9175 (t80) REVERT: C 444 LEU cc_start: 0.9251 (tt) cc_final: 0.8984 (tt) REVERT: C 445 ARG cc_start: 0.9490 (ptt90) cc_final: 0.9211 (ptt90) REVERT: C 466 ILE cc_start: 0.9446 (mt) cc_final: 0.9199 (mt) REVERT: C 469 LEU cc_start: 0.9246 (mt) cc_final: 0.8995 (mt) REVERT: D 81 MET cc_start: 0.7577 (pmm) cc_final: 0.7319 (ppp) REVERT: D 347 PHE cc_start: 0.9436 (t80) cc_final: 0.9020 (t80) REVERT: D 441 LYS cc_start: 0.9504 (ttmt) cc_final: 0.9190 (tttp) REVERT: D 467 ASP cc_start: 0.9212 (m-30) cc_final: 0.8587 (m-30) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1046 time to fit residues: 29.6625 Evaluate side-chains 144 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 140 optimal weight: 0.0170 chunk 63 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 16 optimal weight: 6.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- 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 420 GLN ** A 428 GLN ** 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** C 428 GLN ** 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052775 restraints weight = 65604.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054639 restraints weight = 45880.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055982 restraints weight = 34086.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057049 restraints weight = 26930.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.057873 restraints weight = 22323.802| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13740 Z= 0.144 Angle : 0.723 7.071 18624 Z= 0.370 Chirality : 0.044 0.188 2000 Planarity : 0.005 0.050 2456 Dihedral : 5.246 27.692 1868 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.20), residues: 1672 helix: 0.14 (0.18), residues: 828 sheet: -4.24 (0.51), residues: 56 loop : -3.11 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.011 0.001 TYR D 243 PHE 0.028 0.002 PHE A 255 TRP 0.011 0.002 TRP B 165 HIS 0.007 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00308 (13740) covalent geometry : angle 0.72270 (18624) hydrogen bonds : bond 0.04525 ( 588) hydrogen bonds : angle 5.79433 ( 1728) ********************** 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 194 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.470 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: A 81 MET cc_start: 0.8104 (pmm) cc_final: 0.7737 (ppp) REVERT: A 169 LYS cc_start: 0.8928 (mppt) cc_final: 0.8661 (mppt) REVERT: A 178 HIS cc_start: 0.8979 (m90) cc_final: 0.8733 (m90) REVERT: A 331 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8344 (pt0) REVERT: A 347 PHE cc_start: 0.9564 (t80) cc_final: 0.8986 (t80) REVERT: A 441 LYS cc_start: 0.9400 (ttmm) cc_final: 0.9076 (ttmt) REVERT: B 81 MET cc_start: 0.7631 (pmm) cc_final: 0.7266 (ppp) REVERT: B 178 HIS cc_start: 0.9275 (m-70) cc_final: 0.8945 (m90) REVERT: B 232 TRP cc_start: 0.8882 (t-100) cc_final: 0.8230 (t-100) REVERT: B 329 CYS cc_start: 0.9436 (m) cc_final: 0.8890 (t) REVERT: B 333 LEU cc_start: 0.9329 (mm) cc_final: 0.8633 (tp) REVERT: B 484 ASP cc_start: 0.9586 (t70) cc_final: 0.9222 (t0) REVERT: B 487 ASP cc_start: 0.9699 (t0) cc_final: 0.9428 (p0) REVERT: C 81 MET cc_start: 0.7302 (pmm) cc_final: 0.6886 (ppp) REVERT: C 178 HIS cc_start: 0.9132 (m-70) cc_final: 0.8865 (m-70) REVERT: C 208 GLU cc_start: 0.9661 (pt0) cc_final: 0.9303 (pp20) REVERT: C 347 PHE cc_start: 0.9435 (t80) cc_final: 0.9163 (t80) REVERT: C 444 LEU cc_start: 0.8962 (tt) cc_final: 0.8754 (tt) REVERT: C 469 LEU cc_start: 0.9249 (mt) cc_final: 0.8984 (mt) REVERT: D 81 MET cc_start: 0.7612 (pmm) cc_final: 0.7375 (ppp) REVERT: D 166 PHE cc_start: 0.9526 (p90) cc_final: 0.9279 (p90) REVERT: D 168 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8500 (tpp80) REVERT: D 280 LYS cc_start: 0.9381 (ptpt) cc_final: 0.9145 (pttm) REVERT: D 329 CYS cc_start: 0.9271 (m) cc_final: 0.8906 (m) REVERT: D 333 LEU cc_start: 0.9525 (mm) cc_final: 0.9260 (tp) REVERT: D 347 PHE cc_start: 0.9511 (t80) cc_final: 0.9237 (t80) REVERT: D 466 ILE cc_start: 0.9453 (mt) cc_final: 0.9173 (mt) REVERT: D 467 ASP cc_start: 0.9211 (m-30) cc_final: 0.8822 (m-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1152 time to fit residues: 32.1390 Evaluate side-chains 146 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 151 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 177 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** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 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 = 0.3667 r_free = 0.3667 target = 0.078069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052100 restraints weight = 67674.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053851 restraints weight = 47846.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055074 restraints weight = 36008.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055980 restraints weight = 28964.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056807 restraints weight = 24636.343| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13740 Z= 0.166 Angle : 0.720 7.094 18624 Z= 0.373 Chirality : 0.044 0.184 2000 Planarity : 0.005 0.051 2456 Dihedral : 5.271 27.897 1868 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.20), residues: 1672 helix: 0.12 (0.18), residues: 832 sheet: -4.29 (0.50), residues: 56 loop : -3.08 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.009 0.001 TYR D 243 PHE 0.020 0.002 PHE A 255 TRP 0.016 0.002 TRP B 165 HIS 0.013 0.002 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00346 (13740) covalent geometry : angle 0.72048 (18624) hydrogen bonds : bond 0.04618 ( 588) hydrogen bonds : angle 5.80651 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.95 seconds wall clock time: 37 minutes 35.39 seconds (2255.39 seconds total)