Starting phenix.real_space_refine on Thu Feb 5 18:57:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkz_48343/02_2026/9mkz_48343.cif" } resolution = 3.47 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= 0.001 sd= 0.020 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 S 27 5.16 5 C 6177 2.51 5 N 1629 2.21 5 O 1794 1.98 5 H 9225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18852 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 6284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6284 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 6284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6284 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 6284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6284 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 100 Time building chain proxies: 3.11, per 1000 atoms: 0.16 Number of scatterers: 18852 At special positions: 0 Unit cell: (98.748, 101.28, 127.444, 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) S 27 16.00 O 1794 8.00 N 1629 7.00 C 6177 6.00 H 9225 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 207 " distance=2.03 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: 1.59 Conformation dependent library (CDL) restraints added in 536.4 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 15 sheets defined 48.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 58 through 88 Processing helix chain 'C' and resid 119 through 124 removed outlier: 4.701A pdb=" N LYS C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 148 through 161 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.984A pdb=" N ASN C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 266 through 270 removed outlier: 4.045A pdb=" N GLY C 270 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.592A pdb=" N SER C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.636A pdb=" N TYR C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 362 Processing helix chain 'C' and resid 393 through 405 removed outlier: 3.858A pdb=" N LYS C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 removed outlier: 4.567A pdb=" N ARG C 412 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 removed outlier: 3.521A pdb=" N LEU C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 47 through 57 Processing helix chain 'B' and resid 58 through 88 Processing helix chain 'B' and resid 119 through 124 removed outlier: 4.692A pdb=" N LYS B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 148 through 161 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.977A pdb=" N ASN B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 266 through 270 removed outlier: 4.041A pdb=" N GLY B 270 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.595A pdb=" N SER B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.625A pdb=" N TYR B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.820A pdb=" N LYS B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.838A pdb=" N ARG B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.522A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 88 Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.706A pdb=" N LYS A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.955A pdb=" N ASN A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 266 through 270 removed outlier: 4.044A pdb=" N GLY A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.592A pdb=" N SER A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.626A pdb=" N TYR A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.767A pdb=" N LYS A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 4.416A pdb=" N ARG A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.527A pdb=" N LEU A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing sheet with id=AA1, first strand: chain 'C' and resid 92 through 100 Processing sheet with id=AA2, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.006A pdb=" N LEU C 182 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN C 234 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 184 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET C 277 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 417 " --> pdb=" O MET C 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 100 Processing sheet with id=AA7, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AA8, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA9, first strand: chain 'B' and resid 182 through 186 removed outlier: 5.992A pdb=" N LEU B 182 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B 234 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 184 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET B 277 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 417 " --> pdb=" O MET B 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 366 through 367 Processing sheet with id=AB2, first strand: chain 'A' and resid 92 through 100 Processing sheet with id=AB3, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AB4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AB5, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.023A pdb=" N LEU A 182 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A 234 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 184 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N MET A 277 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 417 " --> pdb=" O MET A 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 366 through 367 518 hydrogen bonds defined for protein. 1437 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: 4.07 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4427 1.03 - 1.23: 5051 1.23 - 1.42: 4741 1.42 - 1.62: 4831 1.62 - 1.81: 33 Bond restraints: 19083 Sorted by residual: bond pdb=" ND1 HIS B 199 " pdb=" CE1 HIS B 199 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.04e+01 bond pdb=" CE1 HIS B 199 " pdb=" NE2 HIS B 199 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.95e+01 bond pdb=" ND1 HIS A 199 " pdb=" CE1 HIS A 199 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" CE1 HIS B 140 " pdb=" NE2 HIS B 140 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.87e+01 bond pdb=" CE1 HIS C 199 " pdb=" NE2 HIS C 199 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.87e+01 ... (remaining 19078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 24379 2.26 - 4.52: 5745 4.52 - 6.78: 2968 6.78 - 9.04: 1046 9.04 - 11.30: 98 Bond angle restraints: 34236 Sorted by residual: angle pdb=" C LYS C 262 " pdb=" N VAL C 263 " pdb=" CA VAL C 263 " ideal model delta sigma weight residual 123.04 130.01 -6.97 9.20e-01 1.18e+00 5.74e+01 angle pdb=" C LYS A 262 " pdb=" N VAL A 263 " pdb=" CA VAL A 263 " ideal model delta sigma weight residual 123.04 129.99 -6.95 9.20e-01 1.18e+00 5.71e+01 angle pdb=" CA ASP B 196 " pdb=" CB ASP B 196 " pdb=" CG ASP B 196 " ideal model delta sigma weight residual 112.60 119.96 -7.36 1.00e+00 1.00e+00 5.42e+01 angle pdb=" CA ASP C 196 " pdb=" CB ASP C 196 " pdb=" CG ASP C 196 " ideal model delta sigma weight residual 112.60 119.93 -7.33 1.00e+00 1.00e+00 5.37e+01 angle pdb=" CA ASN C 206 " pdb=" CB ASN C 206 " pdb=" CG ASN C 206 " ideal model delta sigma weight residual 112.60 119.90 -7.30 1.00e+00 1.00e+00 5.33e+01 ... (remaining 34231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8390 17.90 - 35.79: 416 35.79 - 53.69: 173 53.69 - 71.59: 91 71.59 - 89.48: 20 Dihedral angle restraints: 9090 sinusoidal: 4602 harmonic: 4488 Sorted by residual: dihedral pdb=" N ASP A 196 " pdb=" C ASP A 196 " pdb=" CA ASP A 196 " pdb=" CB ASP A 196 " ideal model delta harmonic sigma weight residual 122.80 134.39 -11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" N ARG A 83 " pdb=" C ARG A 83 " pdb=" CA ARG A 83 " pdb=" CB ARG A 83 " ideal model delta harmonic sigma weight residual 122.80 134.35 -11.55 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" N ARG C 83 " pdb=" C ARG C 83 " pdb=" CA ARG C 83 " pdb=" CB ARG C 83 " ideal model delta harmonic sigma weight residual 122.80 134.35 -11.55 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 9087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 940 0.167 - 0.334: 35 0.334 - 0.500: 208 0.500 - 0.667: 287 0.667 - 0.834: 45 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CG LEU A 451 " pdb=" CB LEU A 451 " pdb=" CD1 LEU A 451 " pdb=" CD2 LEU A 451 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CG LEU B 451 " pdb=" CB LEU B 451 " pdb=" CD1 LEU B 451 " pdb=" CD2 LEU B 451 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CG LEU C 451 " pdb=" CB LEU C 451 " pdb=" CD1 LEU C 451 " pdb=" CD2 LEU C 451 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 1512 not shown) Planarity restraints: 2946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 412 " -0.206 9.50e-02 1.11e+02 1.06e-01 1.49e+02 pdb=" NE ARG C 412 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 412 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 412 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 412 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG C 412 " 0.120 2.00e-02 2.50e+03 pdb="HH12 ARG C 412 " -0.172 2.00e-02 2.50e+03 pdb="HH21 ARG C 412 " -0.020 2.00e-02 2.50e+03 pdb="HH22 ARG C 412 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 100 " -0.116 2.00e-02 2.50e+03 4.49e-02 6.06e+01 pdb=" CG TYR A 100 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 100 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 100 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR A 100 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 100 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 100 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 100 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR A 100 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 100 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 100 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR A 100 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.126 9.50e-02 1.11e+02 6.36e-02 5.28e+01 pdb=" NE ARG A 412 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG A 412 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 412 " -0.099 2.00e-02 2.50e+03 pdb="HH21 ARG A 412 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 412 " 0.065 2.00e-02 2.50e+03 ... (remaining 2943 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 776 2.16 - 2.77: 33120 2.77 - 3.38: 51427 3.38 - 3.99: 65141 3.99 - 4.60: 98543 Nonbonded interactions: 249007 Sorted by model distance: nonbonded pdb=" OD1 ASP B 242 " pdb=" H ASN B 243 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASP A 242 " pdb=" H ASN A 243 " model vdw 1.546 2.450 nonbonded pdb=" OD1 ASP C 242 " pdb=" H ASN C 243 " model vdw 1.546 2.450 nonbonded pdb=" H THR C 119 " pdb=" O ALA C 239 " model vdw 1.578 2.450 nonbonded pdb=" H THR B 119 " pdb=" O ALA B 239 " model vdw 1.582 2.450 ... (remaining 249002 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 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 : 0.034 0.139 9861 Z= 1.771 Angle : 2.571 11.303 13413 Z= 1.679 Chirality : 0.322 0.834 1515 Planarity : 0.010 0.142 1728 Dihedral : 13.859 89.483 3393 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.61 % Allowed : 6.61 % Favored : 92.78 % Cbeta Deviations : 14.20 % 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: 0.02 (0.24), residues: 1260 helix: 0.84 (0.25), residues: 441 sheet: 0.54 (0.28), residues: 264 loop : -0.89 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 227 TYR 0.098 0.016 TYR A 100 PHE 0.045 0.008 PHE C 255 TRP 0.030 0.007 TRP C 295 HIS 0.013 0.001 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.03369 ( 9858) covalent geometry : angle 2.57131 (13407) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.79605 ( 6) hydrogen bonds : bond 0.18221 ( 518) hydrogen bonds : angle 7.11051 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.431 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 SER cc_start: 0.6101 (m) cc_final: 0.5572 (t) REVERT: C 190 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7370 (pttm) REVERT: C 243 ASN cc_start: 0.7421 (t0) cc_final: 0.7006 (t0) REVERT: C 294 PRO cc_start: 0.8122 (Cg_exo) cc_final: 0.7857 (Cg_endo) REVERT: C 378 GLU cc_start: 0.7354 (pt0) cc_final: 0.6979 (pt0) REVERT: C 408 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7391 (ttm-80) REVERT: C 409 LYS cc_start: 0.7917 (tptm) cc_final: 0.7483 (tptp) REVERT: B 95 SER cc_start: 0.6056 (m) cc_final: 0.5537 (t) REVERT: B 97 GLU cc_start: 0.7433 (pm20) cc_final: 0.7192 (pm20) REVERT: B 190 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7379 (pttm) REVERT: B 250 ASP cc_start: 0.7727 (p0) cc_final: 0.7509 (p0) REVERT: B 399 TYR cc_start: 0.6694 (t80) cc_final: 0.6378 (t80) REVERT: B 408 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7067 (ttm-80) REVERT: B 409 LYS cc_start: 0.7746 (tptm) cc_final: 0.7473 (tptm) REVERT: A 95 SER cc_start: 0.5758 (m) cc_final: 0.5201 (t) REVERT: A 97 GLU cc_start: 0.7088 (pm20) cc_final: 0.6739 (pm20) REVERT: A 136 SER cc_start: 0.5159 (p) cc_final: 0.4875 (t) REVERT: A 190 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7409 (pttp) REVERT: A 243 ASN cc_start: 0.7268 (t0) cc_final: 0.6836 (t0) REVERT: A 399 TYR cc_start: 0.6481 (t80) cc_final: 0.6195 (t80) REVERT: A 403 LYS cc_start: 0.7979 (tttm) cc_final: 0.7677 (tttm) REVERT: A 408 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7487 (ttm170) REVERT: A 412 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7930 (ttm110) REVERT: A 419 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6552 (mt-10) REVERT: A 422 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7597 (m-80) outliers start: 6 outliers final: 4 residues processed: 225 average time/residue: 0.2785 time to fit residues: 80.5919 Evaluate side-chains 203 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 451 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138807 restraints weight = 42624.845| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.48 r_work: 0.3777 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9861 Z= 0.178 Angle : 0.590 4.926 13413 Z= 0.326 Chirality : 0.043 0.141 1515 Planarity : 0.004 0.047 1728 Dihedral : 5.840 48.268 1348 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.52 % Allowed : 9.76 % Favored : 88.72 % 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: 0.27 (0.23), residues: 1260 helix: 1.25 (0.23), residues: 474 sheet: 0.62 (0.30), residues: 261 loop : -1.04 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 83 TYR 0.013 0.001 TYR A 100 PHE 0.014 0.002 PHE A 164 TRP 0.006 0.001 TRP A 90 HIS 0.006 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9858) covalent geometry : angle 0.59009 (13407) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.67270 ( 6) hydrogen bonds : bond 0.04121 ( 518) hydrogen bonds : angle 5.52235 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.6483 (mtp) cc_final: 0.6202 (mtp) REVERT: C 162 GLN cc_start: 0.8045 (pm20) cc_final: 0.7775 (pm20) REVERT: C 243 ASN cc_start: 0.7973 (t0) cc_final: 0.7463 (t0) REVERT: C 378 GLU cc_start: 0.7430 (pt0) cc_final: 0.7166 (pt0) REVERT: C 380 ILE cc_start: 0.8588 (pt) cc_final: 0.7424 (pt) REVERT: C 406 GLN cc_start: 0.8216 (mt0) cc_final: 0.7960 (mt0) REVERT: C 414 ASN cc_start: 0.7783 (m-40) cc_final: 0.7431 (m110) REVERT: C 422 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: B 359 GLU cc_start: 0.7960 (tp30) cc_final: 0.7711 (tp30) REVERT: B 422 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: A 90 TRP cc_start: 0.7588 (m-90) cc_final: 0.7270 (m-90) REVERT: A 104 MET cc_start: 0.6430 (mtp) cc_final: 0.6077 (mtp) REVERT: A 136 SER cc_start: 0.7659 (p) cc_final: 0.7425 (t) REVERT: A 243 ASN cc_start: 0.7859 (t0) cc_final: 0.7656 (t0) REVERT: A 403 LYS cc_start: 0.8157 (tttm) cc_final: 0.7936 (tttm) REVERT: A 422 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8328 (m-80) outliers start: 15 outliers final: 6 residues processed: 216 average time/residue: 0.2373 time to fit residues: 67.0201 Evaluate side-chains 199 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 422 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** A 133 HIS ** 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 = 0.4062 r_free = 0.4062 target = 0.154719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131068 restraints weight = 43079.005| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.56 r_work: 0.3640 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9861 Z= 0.215 Angle : 0.566 4.751 13413 Z= 0.313 Chirality : 0.043 0.139 1515 Planarity : 0.004 0.061 1728 Dihedral : 5.781 50.849 1344 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.32 % Allowed : 11.28 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.23), residues: 1260 helix: 1.30 (0.23), residues: 483 sheet: 0.57 (0.30), residues: 255 loop : -1.34 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 83 TYR 0.015 0.002 TYR C 100 PHE 0.018 0.002 PHE C 188 TRP 0.010 0.001 TRP C 295 HIS 0.011 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9858) covalent geometry : angle 0.56543 (13407) SS BOND : bond 0.00914 ( 3) SS BOND : angle 1.15580 ( 6) hydrogen bonds : bond 0.04050 ( 518) hydrogen bonds : angle 5.05238 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.492 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: C 162 GLN cc_start: 0.8285 (pm20) cc_final: 0.8076 (pm20) REVERT: C 243 ASN cc_start: 0.8042 (t0) cc_final: 0.7506 (t0) REVERT: C 250 ASP cc_start: 0.8084 (p0) cc_final: 0.7827 (p0) REVERT: C 295 TRP cc_start: 0.7848 (m-90) cc_final: 0.7582 (m-90) REVERT: C 378 GLU cc_start: 0.7601 (pt0) cc_final: 0.7289 (pt0) REVERT: C 379 GLU cc_start: 0.7130 (tp30) cc_final: 0.6817 (tp30) REVERT: C 380 ILE cc_start: 0.8261 (pt) cc_final: 0.7946 (pt) REVERT: C 406 GLN cc_start: 0.8432 (mt0) cc_final: 0.8227 (mt0) REVERT: C 414 ASN cc_start: 0.7975 (m-40) cc_final: 0.7658 (m110) REVERT: B 165 SER cc_start: 0.7830 (t) cc_final: 0.7592 (t) REVERT: B 250 ASP cc_start: 0.8133 (p0) cc_final: 0.7867 (p0) REVERT: B 359 GLU cc_start: 0.7955 (tp30) cc_final: 0.7753 (tp30) REVERT: A 90 TRP cc_start: 0.7606 (m-90) cc_final: 0.7158 (m-90) REVERT: A 104 MET cc_start: 0.6656 (mtp) cc_final: 0.6456 (mtp) REVERT: A 243 ASN cc_start: 0.7902 (t0) cc_final: 0.7595 (t0) REVERT: A 381 GLU cc_start: 0.8013 (mp0) cc_final: 0.7731 (mp0) REVERT: A 403 LYS cc_start: 0.8318 (tttm) cc_final: 0.8098 (ttmm) REVERT: A 422 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8196 (m-80) outliers start: 13 outliers final: 9 residues processed: 214 average time/residue: 0.2920 time to fit residues: 80.1768 Evaluate side-chains 202 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131076 restraints weight = 42943.543| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.56 r_work: 0.3634 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9861 Z= 0.205 Angle : 0.547 4.997 13413 Z= 0.300 Chirality : 0.042 0.137 1515 Planarity : 0.004 0.066 1728 Dihedral : 5.788 50.679 1344 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.44 % Allowed : 12.09 % Favored : 85.47 % 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: 0.20 (0.24), residues: 1260 helix: 1.48 (0.24), residues: 483 sheet: 0.63 (0.32), residues: 255 loop : -1.45 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 83 TYR 0.015 0.002 TYR C 100 PHE 0.016 0.002 PHE C 188 TRP 0.006 0.001 TRP C 295 HIS 0.007 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9858) covalent geometry : angle 0.54677 (13407) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.06196 ( 6) hydrogen bonds : bond 0.03661 ( 518) hydrogen bonds : angle 4.82913 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.483 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: C 51 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5918 (t70) REVERT: C 104 MET cc_start: 0.6712 (mtp) cc_final: 0.6225 (mtp) REVERT: C 162 GLN cc_start: 0.8276 (pm20) cc_final: 0.8041 (pm20) REVERT: C 243 ASN cc_start: 0.7940 (t0) cc_final: 0.7390 (t0) REVERT: C 250 ASP cc_start: 0.8042 (p0) cc_final: 0.7697 (p0) REVERT: C 295 TRP cc_start: 0.7505 (m-90) cc_final: 0.7301 (m-90) REVERT: C 297 GLU cc_start: 0.7511 (mp0) cc_final: 0.7265 (mp0) REVERT: C 378 GLU cc_start: 0.7685 (pt0) cc_final: 0.7353 (pt0) REVERT: C 379 GLU cc_start: 0.7045 (tp30) cc_final: 0.6685 (tp30) REVERT: C 411 ILE cc_start: 0.8447 (mm) cc_final: 0.8040 (mt) REVERT: C 414 ASN cc_start: 0.8104 (m-40) cc_final: 0.7769 (m110) REVERT: C 422 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: B 165 SER cc_start: 0.7780 (t) cc_final: 0.7543 (t) REVERT: B 295 TRP cc_start: 0.7855 (m-90) cc_final: 0.7028 (m100) REVERT: B 359 GLU cc_start: 0.7979 (tp30) cc_final: 0.7697 (tp30) REVERT: A 90 TRP cc_start: 0.7679 (m-90) cc_final: 0.7222 (m-90) REVERT: A 243 ASN cc_start: 0.7856 (t0) cc_final: 0.7564 (t0) REVERT: A 381 GLU cc_start: 0.7964 (mp0) cc_final: 0.7678 (mp0) REVERT: A 403 LYS cc_start: 0.8296 (tttm) cc_final: 0.8077 (ttmm) REVERT: A 413 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: A 430 THR cc_start: 0.8431 (m) cc_final: 0.8186 (p) outliers start: 24 outliers final: 14 residues processed: 209 average time/residue: 0.3049 time to fit residues: 81.5949 Evaluate side-chains 208 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132269 restraints weight = 42638.791| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.57 r_work: 0.3637 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9861 Z= 0.167 Angle : 0.515 4.948 13413 Z= 0.282 Chirality : 0.041 0.142 1515 Planarity : 0.004 0.061 1728 Dihedral : 5.702 50.974 1344 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.24 % Allowed : 12.91 % Favored : 84.86 % 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: 0.25 (0.24), residues: 1260 helix: 1.60 (0.24), residues: 483 sheet: 0.68 (0.32), residues: 258 loop : -1.56 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 83 TYR 0.013 0.001 TYR C 100 PHE 0.015 0.001 PHE C 188 TRP 0.006 0.001 TRP A 295 HIS 0.006 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9858) covalent geometry : angle 0.51486 (13407) SS BOND : bond 0.00790 ( 3) SS BOND : angle 1.08249 ( 6) hydrogen bonds : bond 0.03509 ( 518) hydrogen bonds : angle 4.73421 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.488 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: C 51 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5953 (t70) REVERT: C 243 ASN cc_start: 0.7937 (t0) cc_final: 0.7353 (t0) REVERT: C 250 ASP cc_start: 0.8069 (p0) cc_final: 0.7686 (p0) REVERT: C 297 GLU cc_start: 0.7455 (mp0) cc_final: 0.7226 (mp0) REVERT: C 378 GLU cc_start: 0.7678 (pt0) cc_final: 0.7341 (pt0) REVERT: C 379 GLU cc_start: 0.7074 (tp30) cc_final: 0.6665 (tp30) REVERT: C 411 ILE cc_start: 0.8452 (mm) cc_final: 0.8033 (mt) REVERT: C 414 ASN cc_start: 0.8107 (m-40) cc_final: 0.7656 (m-40) REVERT: B 165 SER cc_start: 0.7741 (t) cc_final: 0.7512 (t) REVERT: B 295 TRP cc_start: 0.7818 (m-90) cc_final: 0.6984 (m100) REVERT: B 359 GLU cc_start: 0.7980 (tp30) cc_final: 0.7692 (tp30) REVERT: B 409 LYS cc_start: 0.8517 (tptm) cc_final: 0.8146 (tptp) REVERT: A 243 ASN cc_start: 0.7830 (t0) cc_final: 0.7513 (t0) REVERT: A 295 TRP cc_start: 0.7735 (m-90) cc_final: 0.7503 (m-90) REVERT: A 323 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7761 (t-90) REVERT: A 381 GLU cc_start: 0.7921 (mp0) cc_final: 0.7642 (mp0) REVERT: A 403 LYS cc_start: 0.8291 (tttm) cc_final: 0.8060 (ttmm) REVERT: A 413 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: A 430 THR cc_start: 0.8451 (m) cc_final: 0.8201 (p) outliers start: 22 outliers final: 18 residues processed: 213 average time/residue: 0.2762 time to fit residues: 76.0698 Evaluate side-chains 212 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129350 restraints weight = 43275.951| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.63 r_work: 0.3603 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9861 Z= 0.126 Angle : 0.496 4.737 13413 Z= 0.269 Chirality : 0.041 0.147 1515 Planarity : 0.004 0.050 1728 Dihedral : 5.568 50.671 1344 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.03 % Allowed : 13.21 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.24), residues: 1260 helix: 1.82 (0.24), residues: 483 sheet: 0.77 (0.32), residues: 258 loop : -1.44 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 83 TYR 0.015 0.001 TYR A 410 PHE 0.011 0.001 PHE B 164 TRP 0.006 0.001 TRP C 132 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9858) covalent geometry : angle 0.49545 (13407) SS BOND : bond 0.00608 ( 3) SS BOND : angle 0.79944 ( 6) hydrogen bonds : bond 0.03182 ( 518) hydrogen bonds : angle 4.60520 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.514 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: C 51 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5996 (t70) REVERT: C 243 ASN cc_start: 0.7852 (t0) cc_final: 0.7241 (t0) REVERT: C 378 GLU cc_start: 0.7765 (pt0) cc_final: 0.7352 (pt0) REVERT: C 379 GLU cc_start: 0.6974 (tp30) cc_final: 0.6473 (tp30) REVERT: C 406 GLN cc_start: 0.8375 (mt0) cc_final: 0.8106 (mt0) REVERT: C 411 ILE cc_start: 0.8427 (mm) cc_final: 0.8030 (mt) REVERT: C 414 ASN cc_start: 0.7992 (m-40) cc_final: 0.7490 (m-40) REVERT: B 165 SER cc_start: 0.7602 (t) cc_final: 0.7354 (t) REVERT: B 295 TRP cc_start: 0.7801 (m-90) cc_final: 0.7263 (m100) REVERT: B 359 GLU cc_start: 0.8061 (tp30) cc_final: 0.7741 (tp30) REVERT: B 417 LYS cc_start: 0.8393 (tttt) cc_final: 0.8089 (tttp) REVERT: A 96 ILE cc_start: 0.8239 (tt) cc_final: 0.8007 (tt) REVERT: A 243 ASN cc_start: 0.7831 (t0) cc_final: 0.7439 (t0) REVERT: A 295 TRP cc_start: 0.7687 (m-90) cc_final: 0.7459 (m-90) REVERT: A 323 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: A 381 GLU cc_start: 0.7932 (mp0) cc_final: 0.7641 (mp0) REVERT: A 403 LYS cc_start: 0.8286 (tttm) cc_final: 0.8002 (ttmm) REVERT: A 413 GLU cc_start: 0.7694 (tp30) cc_final: 0.7063 (tp30) outliers start: 20 outliers final: 12 residues processed: 206 average time/residue: 0.2865 time to fit residues: 75.9689 Evaluate side-chains 205 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.153901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129440 restraints weight = 43318.257| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.62 r_work: 0.3595 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9861 Z= 0.122 Angle : 0.489 5.258 13413 Z= 0.265 Chirality : 0.041 0.146 1515 Planarity : 0.004 0.045 1728 Dihedral : 5.460 51.251 1344 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.93 % Allowed : 13.72 % Favored : 84.35 % 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: 0.57 (0.24), residues: 1260 helix: 1.96 (0.24), residues: 483 sheet: 0.81 (0.32), residues: 255 loop : -1.43 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 412 TYR 0.013 0.001 TYR C 100 PHE 0.011 0.001 PHE B 164 TRP 0.005 0.001 TRP C 132 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9858) covalent geometry : angle 0.48894 (13407) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.64050 ( 6) hydrogen bonds : bond 0.03051 ( 518) hydrogen bonds : angle 4.50764 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.525 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: C 51 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5985 (t70) REVERT: C 184 ASP cc_start: 0.8400 (t0) cc_final: 0.8178 (t0) REVERT: C 243 ASN cc_start: 0.7774 (t0) cc_final: 0.7292 (t0) REVERT: C 378 GLU cc_start: 0.7831 (pt0) cc_final: 0.7409 (pt0) REVERT: C 379 GLU cc_start: 0.6945 (tp30) cc_final: 0.6422 (tp30) REVERT: C 411 ILE cc_start: 0.8396 (mm) cc_final: 0.7994 (mt) REVERT: C 414 ASN cc_start: 0.7979 (m-40) cc_final: 0.7453 (m-40) REVERT: B 165 SER cc_start: 0.7505 (t) cc_final: 0.7263 (t) REVERT: B 295 TRP cc_start: 0.7765 (m-90) cc_final: 0.7242 (m100) REVERT: B 359 GLU cc_start: 0.8046 (tp30) cc_final: 0.7711 (tp30) REVERT: B 380 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.7510 (pt) REVERT: B 409 LYS cc_start: 0.8381 (tptm) cc_final: 0.8037 (tptp) REVERT: A 96 ILE cc_start: 0.8244 (tt) cc_final: 0.8041 (tt) REVERT: A 243 ASN cc_start: 0.7823 (t0) cc_final: 0.7427 (t0) REVERT: A 295 TRP cc_start: 0.7644 (m-90) cc_final: 0.7410 (m-90) REVERT: A 323 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7722 (t-90) REVERT: A 381 GLU cc_start: 0.7935 (mp0) cc_final: 0.7642 (mp0) REVERT: A 403 LYS cc_start: 0.8252 (tttm) cc_final: 0.7955 (ttmm) REVERT: A 413 GLU cc_start: 0.7700 (tp30) cc_final: 0.7037 (tp30) outliers start: 19 outliers final: 15 residues processed: 205 average time/residue: 0.3025 time to fit residues: 79.8288 Evaluate side-chains 209 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 HIS ** 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 = 0.3996 r_free = 0.3996 target = 0.151487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127310 restraints weight = 43185.943| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.60 r_work: 0.3562 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9861 Z= 0.233 Angle : 0.563 6.764 13413 Z= 0.307 Chirality : 0.042 0.151 1515 Planarity : 0.005 0.079 1728 Dihedral : 5.672 52.727 1344 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.03 % Allowed : 15.04 % Favored : 82.93 % 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: 0.30 (0.24), residues: 1260 helix: 1.71 (0.24), residues: 483 sheet: 0.73 (0.32), residues: 261 loop : -1.61 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 412 TYR 0.014 0.002 TYR A 100 PHE 0.018 0.002 PHE C 188 TRP 0.005 0.001 TRP A 132 HIS 0.008 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 9858) covalent geometry : angle 0.56238 (13407) SS BOND : bond 0.00975 ( 3) SS BOND : angle 0.91918 ( 6) hydrogen bonds : bond 0.03619 ( 518) hydrogen bonds : angle 4.61488 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.522 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: C 51 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5938 (t70) REVERT: C 184 ASP cc_start: 0.8397 (t0) cc_final: 0.8192 (t0) REVERT: C 243 ASN cc_start: 0.7794 (t0) cc_final: 0.7343 (t0) REVERT: C 378 GLU cc_start: 0.7925 (pt0) cc_final: 0.7490 (pt0) REVERT: C 379 GLU cc_start: 0.7068 (tp30) cc_final: 0.6550 (tp30) REVERT: C 406 GLN cc_start: 0.8322 (mt0) cc_final: 0.8088 (mt0) REVERT: C 411 ILE cc_start: 0.8441 (mm) cc_final: 0.8055 (mt) REVERT: C 414 ASN cc_start: 0.8022 (m-40) cc_final: 0.7548 (m-40) REVERT: B 87 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6880 (t80) REVERT: B 165 SER cc_start: 0.7631 (t) cc_final: 0.7385 (t) REVERT: B 295 TRP cc_start: 0.7786 (m-90) cc_final: 0.6813 (m100) REVERT: B 359 GLU cc_start: 0.8021 (tp30) cc_final: 0.7693 (tp30) REVERT: B 379 GLU cc_start: 0.7187 (tp30) cc_final: 0.6965 (tp30) REVERT: B 380 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7854 (pt) REVERT: B 413 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: A 96 ILE cc_start: 0.8354 (tt) cc_final: 0.8152 (tt) REVERT: A 243 ASN cc_start: 0.7816 (t0) cc_final: 0.7420 (t0) REVERT: A 403 LYS cc_start: 0.8261 (tttm) cc_final: 0.7984 (ttmm) REVERT: A 413 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7087 (tp30) outliers start: 20 outliers final: 12 residues processed: 201 average time/residue: 0.3084 time to fit residues: 79.9567 Evaluate side-chains 203 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** 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 = 0.4026 r_free = 0.4026 target = 0.154490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129746 restraints weight = 42911.498| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.64 r_work: 0.3596 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9861 Z= 0.125 Angle : 0.517 7.941 13413 Z= 0.277 Chirality : 0.041 0.148 1515 Planarity : 0.004 0.073 1728 Dihedral : 5.470 51.146 1344 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.73 % Allowed : 15.65 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.24), residues: 1260 helix: 1.93 (0.24), residues: 483 sheet: 0.71 (0.32), residues: 255 loop : -1.47 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 412 TYR 0.013 0.001 TYR C 100 PHE 0.011 0.001 PHE C 188 TRP 0.007 0.001 TRP A 132 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9858) covalent geometry : angle 0.51676 (13407) SS BOND : bond 0.00531 ( 3) SS BOND : angle 0.66686 ( 6) hydrogen bonds : bond 0.03108 ( 518) hydrogen bonds : angle 4.46292 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.454 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: C 165 SER cc_start: 0.7785 (t) cc_final: 0.7521 (t) REVERT: C 184 ASP cc_start: 0.8372 (t0) cc_final: 0.8030 (t70) REVERT: C 243 ASN cc_start: 0.7752 (t0) cc_final: 0.7310 (t0) REVERT: C 256 VAL cc_start: 0.8492 (p) cc_final: 0.8265 (t) REVERT: C 379 GLU cc_start: 0.7020 (tp30) cc_final: 0.6450 (tp30) REVERT: C 406 GLN cc_start: 0.8292 (mt0) cc_final: 0.8089 (mt0) REVERT: C 411 ILE cc_start: 0.8420 (mm) cc_final: 0.8036 (mt) REVERT: C 414 ASN cc_start: 0.8004 (m-40) cc_final: 0.7480 (m-40) REVERT: B 87 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6851 (t80) REVERT: B 165 SER cc_start: 0.7549 (t) cc_final: 0.7306 (t) REVERT: B 295 TRP cc_start: 0.7720 (m-90) cc_final: 0.6703 (m100) REVERT: B 359 GLU cc_start: 0.8003 (tp30) cc_final: 0.7663 (tp30) REVERT: B 379 GLU cc_start: 0.7120 (tp30) cc_final: 0.6853 (tp30) REVERT: B 380 ILE cc_start: 0.8211 (pt) cc_final: 0.7792 (pt) REVERT: B 409 LYS cc_start: 0.8426 (tptm) cc_final: 0.7842 (tptm) REVERT: B 413 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 243 ASN cc_start: 0.7791 (t0) cc_final: 0.7380 (t0) REVERT: A 403 LYS cc_start: 0.8235 (tttm) cc_final: 0.7963 (ttmm) REVERT: A 413 GLU cc_start: 0.7649 (tp30) cc_final: 0.7022 (tp30) outliers start: 17 outliers final: 14 residues processed: 199 average time/residue: 0.2703 time to fit residues: 68.9877 Evaluate side-chains 205 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 0.0770 chunk 33 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130514 restraints weight = 43112.278| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.59 r_work: 0.3613 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9861 Z= 0.108 Angle : 0.498 6.595 13413 Z= 0.266 Chirality : 0.041 0.149 1515 Planarity : 0.004 0.036 1728 Dihedral : 5.314 50.556 1344 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.73 % Allowed : 15.04 % Favored : 83.23 % 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: 0.69 (0.25), residues: 1260 helix: 2.14 (0.24), residues: 483 sheet: 0.77 (0.32), residues: 261 loop : -1.42 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 412 TYR 0.013 0.001 TYR A 100 PHE 0.010 0.001 PHE B 164 TRP 0.006 0.001 TRP C 132 HIS 0.006 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9858) covalent geometry : angle 0.49796 (13407) SS BOND : bond 0.00472 ( 3) SS BOND : angle 0.59948 ( 6) hydrogen bonds : bond 0.02862 ( 518) hydrogen bonds : angle 4.36219 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue VAL 67 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue ILE 458 is missing expected H atoms. Skipping. Residue THR 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue ILE 464 is missing expected H atoms. Skipping. Residue TYR 466 is missing expected H atoms. Skipping. Residue LEU 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.493 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: C 165 SER cc_start: 0.7741 (t) cc_final: 0.7490 (t) REVERT: C 184 ASP cc_start: 0.8378 (t0) cc_final: 0.8039 (t70) REVERT: C 243 ASN cc_start: 0.7716 (t0) cc_final: 0.7282 (t0) REVERT: C 379 GLU cc_start: 0.7001 (tp30) cc_final: 0.6433 (tp30) REVERT: C 394 GLN cc_start: 0.7881 (mt0) cc_final: 0.7676 (mt0) REVERT: C 411 ILE cc_start: 0.8388 (mm) cc_final: 0.8008 (mt) REVERT: C 414 ASN cc_start: 0.7973 (m-40) cc_final: 0.7457 (m-40) REVERT: B 87 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6838 (t80) REVERT: B 165 SER cc_start: 0.7416 (t) cc_final: 0.7198 (t) REVERT: B 295 TRP cc_start: 0.7678 (m-90) cc_final: 0.6676 (m100) REVERT: B 359 GLU cc_start: 0.8038 (tp30) cc_final: 0.7709 (tp30) REVERT: B 379 GLU cc_start: 0.7196 (tp30) cc_final: 0.6890 (tp30) REVERT: B 380 ILE cc_start: 0.8209 (pt) cc_final: 0.7762 (pt) REVERT: B 413 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 243 ASN cc_start: 0.7768 (t0) cc_final: 0.7250 (t0) REVERT: A 403 LYS cc_start: 0.8203 (tttm) cc_final: 0.7945 (ttmm) REVERT: A 413 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7049 (tp30) outliers start: 17 outliers final: 13 residues processed: 196 average time/residue: 0.2820 time to fit residues: 71.4678 Evaluate side-chains 205 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129502 restraints weight = 43042.936| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.63 r_work: 0.3591 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9861 Z= 0.130 Angle : 0.504 6.353 13413 Z= 0.271 Chirality : 0.041 0.149 1515 Planarity : 0.004 0.042 1728 Dihedral : 5.284 50.705 1344 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.52 % Allowed : 15.35 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1260 helix: 2.16 (0.24), residues: 483 sheet: 0.77 (0.32), residues: 261 loop : -1.48 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 412 TYR 0.012 0.001 TYR A 100 PHE 0.011 0.001 PHE B 164 TRP 0.005 0.001 TRP A 132 HIS 0.019 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9858) covalent geometry : angle 0.50414 (13407) SS BOND : bond 0.00558 ( 3) SS BOND : angle 0.67229 ( 6) hydrogen bonds : bond 0.03003 ( 518) hydrogen bonds : angle 4.36000 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4559.03 seconds wall clock time: 78 minutes 2.93 seconds (4682.93 seconds total)