Starting phenix.real_space_refine on Wed Mar 4 03:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xox_22283/03_2026/6xox_22283.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 64 5.16 5 C 6778 2.51 5 N 1828 2.21 5 O 1957 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10629 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "R" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'V6G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.26 Number of scatterers: 10629 At special positions: 0 Unit cell: (159.12, 113.36, 101.92, 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 64 16.00 F 2 9.00 O 1957 8.00 N 1828 7.00 C 6778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 1.02 Conformation dependent library (CDL) restraints added in 689.4 milliseconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 33.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.501A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.608A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 241 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.027A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.543A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.735A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.056A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.537A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.664A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.947A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 Processing helix chain 'R' and resid 136 through 141 removed outlier: 3.736A pdb=" N LEU R 141 " --> pdb=" O PRO R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 168 Processing helix chain 'R' and resid 174 through 210 removed outlier: 4.209A pdb=" N GLN R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 223 WARNING: missing atoms! Processing helix chain 'R' and resid 223 through 256 removed outlier: 4.155A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 removed outlier: 3.504A pdb=" N ILE R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 4.124A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 378 through 403 removed outlier: 4.217A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 214 removed outlier: 3.576A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.753A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.744A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.744A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.757A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.560A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.316A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.691A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.188A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.188A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 6.686A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.740A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 79 through 83 521 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3110 1.33 - 1.45: 2339 1.45 - 1.57: 5339 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 10876 Sorted by residual: bond pdb=" C08 V6G R 501 " pdb=" C15 V6G R 501 " ideal model delta sigma weight residual 1.496 1.433 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C09 V6G R 501 " pdb=" N01 V6G R 501 " ideal model delta sigma weight residual 1.426 1.483 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.40e+00 bond pdb=" C19 V6G R 501 " pdb=" C22 V6G R 501 " ideal model delta sigma weight residual 1.373 1.320 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C38 V6G R 501 " pdb=" C39 V6G R 501 " ideal model delta sigma weight residual 1.406 1.356 0.050 2.00e-02 2.50e+03 6.15e+00 ... (remaining 10871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13987 2.26 - 4.52: 666 4.52 - 6.78: 99 6.78 - 9.04: 20 9.04 - 11.31: 6 Bond angle restraints: 14778 Sorted by residual: angle pdb=" N ILE B 80 " pdb=" CA ILE B 80 " pdb=" C ILE B 80 " ideal model delta sigma weight residual 107.75 116.93 -9.18 1.46e+00 4.69e-01 3.95e+01 angle pdb=" N TYR R 69 " pdb=" CA TYR R 69 " pdb=" C TYR R 69 " ideal model delta sigma weight residual 114.62 108.79 5.83 1.14e+00 7.69e-01 2.62e+01 angle pdb=" C GLY R 377 " pdb=" N THR R 378 " pdb=" CA THR R 378 " ideal model delta sigma weight residual 121.54 130.36 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C ARG R 299 " pdb=" N ASN R 300 " pdb=" CA ASN R 300 " ideal model delta sigma weight residual 122.82 129.15 -6.33 1.42e+00 4.96e-01 1.99e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 114.16 6.98 1.75e+00 3.27e-01 1.59e+01 ... (remaining 14773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6075 17.76 - 35.53: 283 35.53 - 53.29: 60 53.29 - 71.05: 7 71.05 - 88.82: 8 Dihedral angle restraints: 6433 sinusoidal: 2494 harmonic: 3939 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -174.82 88.82 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.53 41.47 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -127.36 41.36 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 6430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1290 0.076 - 0.152: 310 0.152 - 0.227: 31 0.227 - 0.303: 7 0.303 - 0.379: 3 Chirality restraints: 1641 Sorted by residual: chirality pdb=" CG LEU R 159 " pdb=" CB LEU R 159 " pdb=" CD1 LEU R 159 " pdb=" CD2 LEU R 159 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C20 V6G R 501 " pdb=" C19 V6G R 501 " pdb=" C21 V6G R 501 " pdb=" N04 V6G R 501 " both_signs ideal model delta sigma weight residual False 2.46 2.77 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1638 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO G 49 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.024 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR R 242 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" CG ASN A 239 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " 0.015 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1994 2.76 - 3.29: 9986 3.29 - 3.83: 18495 3.83 - 4.36: 21485 4.36 - 4.90: 36885 Nonbonded interactions: 88845 Sorted by model distance: nonbonded pdb=" N SER R 31 " pdb=" OE2 GLU R 34 " model vdw 2.223 3.120 nonbonded pdb=" OD2 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.250 3.040 nonbonded pdb=" O GLY R 295 " pdb=" OG1 THR R 298 " model vdw 2.273 3.040 ... (remaining 88840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.011 0.090 10884 Z= 0.484 Angle : 1.101 11.306 14794 Z= 0.592 Chirality : 0.065 0.379 1641 Planarity : 0.007 0.071 1868 Dihedral : 11.421 77.788 3869 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.99 % Allowed : 4.41 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.29 (0.19), residues: 1328 helix: -2.03 (0.19), residues: 422 sheet: -2.23 (0.24), residues: 345 loop : -2.07 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 68 TYR 0.045 0.004 TYR R 242 PHE 0.038 0.004 PHE E 227 TRP 0.039 0.004 TRP E 111 HIS 0.019 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.01107 (10876) covalent geometry : angle 1.10023 (14778) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.60299 ( 16) hydrogen bonds : bond 0.11712 ( 508) hydrogen bonds : angle 6.97543 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 262 time to evaluate : 0.386 Fit side-chains REVERT: A 239 ASN cc_start: 0.8692 (p0) cc_final: 0.8472 (p0) REVERT: A 270 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9351 (mm) REVERT: A 289 LEU cc_start: 0.9201 (tp) cc_final: 0.8950 (tp) REVERT: A 295 ASP cc_start: 0.7729 (p0) cc_final: 0.7085 (m-30) REVERT: A 296 LEU cc_start: 0.8347 (mp) cc_final: 0.7990 (mt) REVERT: A 378 ASP cc_start: 0.7952 (m-30) cc_final: 0.7582 (m-30) REVERT: B 32 GLN cc_start: 0.8224 (mt0) cc_final: 0.8017 (mt0) REVERT: B 262 MET cc_start: 0.7726 (tpp) cc_final: 0.7377 (ttt) REVERT: E 222 GLU cc_start: 0.7534 (pt0) cc_final: 0.7290 (pt0) REVERT: G 36 ASP cc_start: 0.7983 (m-30) cc_final: 0.7747 (m-30) REVERT: N 87 LYS cc_start: 0.8997 (mttt) cc_final: 0.8619 (mtpt) REVERT: N 125 THR cc_start: 0.9106 (m) cc_final: 0.8818 (t) REVERT: R 192 LEU cc_start: 0.9026 (tp) cc_final: 0.8802 (tt) outliers start: 11 outliers final: 4 residues processed: 271 average time/residue: 0.1197 time to fit residues: 43.9029 Evaluate side-chains 164 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 213 GLN A 220 HIS A 357 HIS B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN E 174 GLN G 44 HIS N 35 ASN N 120 GLN R 240 ASN R 304 ASN R 320 ASN R 363 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.079383 restraints weight = 25569.315| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.72 r_work: 0.3162 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10884 Z= 0.139 Angle : 0.638 11.521 14794 Z= 0.334 Chirality : 0.044 0.174 1641 Planarity : 0.005 0.064 1868 Dihedral : 5.863 59.940 1550 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.06 % Allowed : 8.91 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.75 (0.22), residues: 1328 helix: -0.01 (0.24), residues: 423 sheet: -1.89 (0.25), residues: 357 loop : -1.41 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 44 TYR 0.023 0.002 TYR R 148 PHE 0.023 0.002 PHE R 280 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00301 (10876) covalent geometry : angle 0.63764 (14778) SS BOND : bond 0.00200 ( 8) SS BOND : angle 0.87993 ( 16) hydrogen bonds : bond 0.04039 ( 508) hydrogen bonds : angle 5.26323 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8738 (p0) cc_final: 0.8347 (p0) REVERT: A 344 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 262 MET cc_start: 0.8189 (tpp) cc_final: 0.7785 (ttt) REVERT: B 273 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8221 (pt) REVERT: E 85 SER cc_start: 0.9273 (m) cc_final: 0.8869 (p) REVERT: E 171 GLN cc_start: 0.8385 (mp10) cc_final: 0.7941 (mp10) REVERT: E 212 VAL cc_start: 0.8138 (t) cc_final: 0.7906 (p) REVERT: E 222 GLU cc_start: 0.8242 (pt0) cc_final: 0.8040 (pp20) REVERT: N 73 ASP cc_start: 0.7634 (t0) cc_final: 0.7347 (t0) REVERT: N 82 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7466 (tp40) REVERT: N 87 LYS cc_start: 0.9079 (mttt) cc_final: 0.8835 (mtmt) REVERT: N 89 GLU cc_start: 0.8851 (pm20) cc_final: 0.8472 (pm20) REVERT: N 90 ASP cc_start: 0.8324 (m-30) cc_final: 0.7624 (m-30) REVERT: R 272 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8913 (mp) REVERT: R 413 PHE cc_start: 0.7575 (m-80) cc_final: 0.7331 (m-80) outliers start: 34 outliers final: 13 residues processed: 243 average time/residue: 0.0945 time to fit residues: 33.3671 Evaluate side-chains 188 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.101966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079171 restraints weight = 25875.414| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.75 r_work: 0.3166 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10884 Z= 0.132 Angle : 0.603 13.384 14794 Z= 0.311 Chirality : 0.043 0.150 1641 Planarity : 0.004 0.062 1868 Dihedral : 5.145 55.847 1544 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.24 % Allowed : 11.16 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.08 (0.23), residues: 1328 helix: 0.77 (0.25), residues: 423 sheet: -1.69 (0.25), residues: 357 loop : -1.07 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.021 0.001 TYR R 148 PHE 0.022 0.001 PHE A 345 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00291 (10876) covalent geometry : angle 0.60250 (14778) SS BOND : bond 0.00143 ( 8) SS BOND : angle 0.82081 ( 16) hydrogen bonds : bond 0.03714 ( 508) hydrogen bonds : angle 4.88342 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7032 (mp) cc_final: 0.6529 (mp) REVERT: A 297 LEU cc_start: 0.7002 (tp) cc_final: 0.6799 (tt) REVERT: A 358 TYR cc_start: 0.8279 (m-80) cc_final: 0.8074 (m-80) REVERT: A 372 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8903 (mt) REVERT: E 128 MET cc_start: 0.8329 (mmm) cc_final: 0.8078 (mmm) REVERT: E 171 GLN cc_start: 0.8438 (mp10) cc_final: 0.7984 (mp10) REVERT: E 212 VAL cc_start: 0.8062 (t) cc_final: 0.7850 (p) REVERT: E 222 GLU cc_start: 0.8159 (pt0) cc_final: 0.7871 (pp20) REVERT: G 22 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7891 (tm-30) REVERT: N 82 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7503 (tp40) REVERT: N 87 LYS cc_start: 0.9044 (mttt) cc_final: 0.8773 (mtmt) REVERT: N 89 GLU cc_start: 0.8860 (pm20) cc_final: 0.8641 (pm20) REVERT: N 90 ASP cc_start: 0.8401 (m-30) cc_final: 0.7647 (m-30) outliers start: 36 outliers final: 15 residues processed: 223 average time/residue: 0.0954 time to fit residues: 30.7596 Evaluate side-chains 181 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 68 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 271 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.102042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079584 restraints weight = 25731.092| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.70 r_work: 0.3167 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10884 Z= 0.129 Angle : 0.593 11.220 14794 Z= 0.306 Chirality : 0.042 0.152 1641 Planarity : 0.004 0.063 1868 Dihedral : 4.878 53.204 1543 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.88 % Allowed : 13.05 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.56 (0.24), residues: 1328 helix: 1.33 (0.26), residues: 423 sheet: -1.51 (0.25), residues: 349 loop : -0.82 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 206 TYR 0.019 0.001 TYR R 148 PHE 0.017 0.001 PHE A 345 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00285 (10876) covalent geometry : angle 0.59260 (14778) SS BOND : bond 0.00472 ( 8) SS BOND : angle 0.97766 ( 16) hydrogen bonds : bond 0.03541 ( 508) hydrogen bonds : angle 4.67953 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7010 (mp) cc_final: 0.6585 (mp) REVERT: A 358 TYR cc_start: 0.8296 (m-80) cc_final: 0.8022 (m-80) REVERT: A 372 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8931 (mt) REVERT: B 262 MET cc_start: 0.8020 (tpp) cc_final: 0.7720 (ttt) REVERT: E 128 MET cc_start: 0.8449 (mmm) cc_final: 0.7986 (mmm) REVERT: E 171 GLN cc_start: 0.8505 (mp10) cc_final: 0.8092 (mp10) REVERT: E 206 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7482 (ptt-90) REVERT: E 212 VAL cc_start: 0.8122 (t) cc_final: 0.7890 (p) REVERT: E 222 GLU cc_start: 0.8186 (pt0) cc_final: 0.7840 (pp20) REVERT: G 14 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7932 (ptmm) REVERT: G 22 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7892 (tm-30) REVERT: N 90 ASP cc_start: 0.8392 (m-30) cc_final: 0.7709 (m-30) REVERT: R 38 LYS cc_start: 0.9497 (mtmt) cc_final: 0.8964 (ttmm) REVERT: R 165 ILE cc_start: 0.8851 (tp) cc_final: 0.8639 (pt) REVERT: R 272 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8922 (mp) REVERT: R 407 ASN cc_start: 0.8480 (t0) cc_final: 0.8057 (t0) outliers start: 32 outliers final: 18 residues processed: 212 average time/residue: 0.0966 time to fit residues: 29.6233 Evaluate side-chains 183 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 6 GLN B 9 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.101494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078759 restraints weight = 25896.959| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.72 r_work: 0.3155 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10884 Z= 0.147 Angle : 0.616 11.897 14794 Z= 0.317 Chirality : 0.043 0.224 1641 Planarity : 0.004 0.061 1868 Dihedral : 4.839 51.777 1543 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.97 % Allowed : 13.77 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.34 (0.24), residues: 1328 helix: 1.55 (0.26), residues: 423 sheet: -1.31 (0.25), residues: 356 loop : -0.76 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.017 0.001 TYR R 148 PHE 0.014 0.001 PHE A 345 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00329 (10876) covalent geometry : angle 0.60827 (14778) SS BOND : bond 0.00316 ( 8) SS BOND : angle 3.03151 ( 16) hydrogen bonds : bond 0.03537 ( 508) hydrogen bonds : angle 4.58385 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.404 Fit side-chains REVERT: A 56 ILE cc_start: 0.7141 (mp) cc_final: 0.6771 (mp) REVERT: A 358 TYR cc_start: 0.8302 (m-80) cc_final: 0.8048 (m-80) REVERT: A 360 TYR cc_start: 0.9056 (m-80) cc_final: 0.8710 (m-80) REVERT: A 372 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8941 (mt) REVERT: B 10 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7960 (mp0) REVERT: B 101 MET cc_start: 0.9262 (mtp) cc_final: 0.9027 (mtp) REVERT: E 21 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8451 (p) REVERT: E 128 MET cc_start: 0.8589 (mmm) cc_final: 0.7882 (mmm) REVERT: E 171 GLN cc_start: 0.8477 (mp10) cc_final: 0.7938 (mp10) REVERT: E 222 GLU cc_start: 0.8183 (pt0) cc_final: 0.7835 (pp20) REVERT: G 14 LYS cc_start: 0.8181 (ptmt) cc_final: 0.7960 (ptmm) REVERT: G 22 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7847 (tm-30) REVERT: G 32 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8548 (tmtt) REVERT: N 47 TRP cc_start: 0.8909 (t60) cc_final: 0.8696 (t60) REVERT: N 82 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7373 (tp40) REVERT: R 38 LYS cc_start: 0.9442 (mtmt) cc_final: 0.8927 (ttmm) REVERT: R 407 ASN cc_start: 0.8499 (t0) cc_final: 0.8070 (t0) outliers start: 33 outliers final: 20 residues processed: 198 average time/residue: 0.0932 time to fit residues: 27.1049 Evaluate side-chains 188 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078058 restraints weight = 25995.388| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.74 r_work: 0.3142 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10884 Z= 0.162 Angle : 0.621 10.758 14794 Z= 0.319 Chirality : 0.043 0.171 1641 Planarity : 0.004 0.061 1868 Dihedral : 4.855 50.632 1543 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.79 % Allowed : 15.12 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.18 (0.24), residues: 1328 helix: 1.66 (0.26), residues: 423 sheet: -1.19 (0.26), residues: 354 loop : -0.69 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 206 TYR 0.016 0.002 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00365 (10876) covalent geometry : angle 0.61577 (14778) SS BOND : bond 0.00351 ( 8) SS BOND : angle 2.61700 ( 16) hydrogen bonds : bond 0.03550 ( 508) hydrogen bonds : angle 4.54934 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7152 (mp) cc_final: 0.6845 (mp) REVERT: A 358 TYR cc_start: 0.8302 (m-80) cc_final: 0.8068 (m-80) REVERT: A 372 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8952 (mt) REVERT: B 10 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7882 (mp0) REVERT: B 101 MET cc_start: 0.9251 (mtp) cc_final: 0.9019 (mtp) REVERT: B 314 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8205 (ptt180) REVERT: E 171 GLN cc_start: 0.8496 (mp10) cc_final: 0.7927 (mp10) REVERT: E 206 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7796 (ttp80) REVERT: E 222 GLU cc_start: 0.8192 (pt0) cc_final: 0.7858 (pp20) REVERT: E 234 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8174 (mp0) REVERT: G 14 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7960 (ptmm) REVERT: G 22 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7849 (tm-30) REVERT: G 32 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8573 (tmtt) REVERT: N 82 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7285 (tp40) REVERT: N 117 TYR cc_start: 0.8455 (m-80) cc_final: 0.8009 (m-80) REVERT: R 38 LYS cc_start: 0.9457 (mtmt) cc_final: 0.8939 (ttmm) REVERT: R 152 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: R 195 PHE cc_start: 0.8999 (m-10) cc_final: 0.8751 (m-10) REVERT: R 403 CYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8239 (t) REVERT: R 407 ASN cc_start: 0.8560 (t0) cc_final: 0.8134 (t0) outliers start: 31 outliers final: 19 residues processed: 189 average time/residue: 0.0966 time to fit residues: 26.5545 Evaluate side-chains 180 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079058 restraints weight = 25429.703| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.74 r_work: 0.3161 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10884 Z= 0.172 Angle : 0.620 11.569 14794 Z= 0.318 Chirality : 0.043 0.163 1641 Planarity : 0.004 0.065 1868 Dihedral : 4.842 50.235 1543 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.51 % Allowed : 14.31 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.10 (0.24), residues: 1328 helix: 1.69 (0.26), residues: 423 sheet: -1.13 (0.26), residues: 348 loop : -0.63 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.015 0.001 TYR R 148 PHE 0.014 0.001 PHE R 280 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00389 (10876) covalent geometry : angle 0.61526 (14778) SS BOND : bond 0.00250 ( 8) SS BOND : angle 2.46918 ( 16) hydrogen bonds : bond 0.03572 ( 508) hydrogen bonds : angle 4.53315 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7224 (mp) cc_final: 0.6912 (mp) REVERT: A 358 TYR cc_start: 0.8315 (m-80) cc_final: 0.8066 (m-80) REVERT: A 372 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8986 (mt) REVERT: B 10 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7849 (mp0) REVERT: B 101 MET cc_start: 0.9247 (mtp) cc_final: 0.9001 (mtp) REVERT: B 314 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8254 (ptt180) REVERT: E 126 ILE cc_start: 0.8535 (mm) cc_final: 0.8329 (mp) REVERT: E 189 ASP cc_start: 0.8601 (p0) cc_final: 0.8327 (p0) REVERT: E 206 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7739 (ptt-90) REVERT: G 14 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7965 (ptmm) REVERT: G 22 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7754 (tm-30) REVERT: N 34 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8678 (mmm) REVERT: N 82 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7284 (tp40) REVERT: N 117 TYR cc_start: 0.8463 (m-80) cc_final: 0.8061 (m-80) REVERT: R 37 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: R 152 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: R 195 PHE cc_start: 0.8945 (m-10) cc_final: 0.8715 (m-10) REVERT: R 221 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: R 403 CYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8259 (t) REVERT: R 407 ASN cc_start: 0.8537 (t0) cc_final: 0.8231 (t0) REVERT: R 411 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8415 (tt) outliers start: 39 outliers final: 20 residues processed: 199 average time/residue: 0.0958 time to fit residues: 27.8605 Evaluate side-chains 188 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.0060 chunk 42 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 128 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081430 restraints weight = 25272.153| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.71 r_work: 0.3199 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10884 Z= 0.117 Angle : 0.608 10.662 14794 Z= 0.310 Chirality : 0.042 0.165 1641 Planarity : 0.004 0.065 1868 Dihedral : 4.670 50.514 1543 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.34 % Allowed : 16.02 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.11 (0.24), residues: 1328 helix: 1.87 (0.25), residues: 417 sheet: -0.92 (0.26), residues: 360 loop : -0.53 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.016 0.001 TYR A 318 PHE 0.013 0.001 PHE R 280 TRP 0.015 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 (10876) covalent geometry : angle 0.60334 (14778) SS BOND : bond 0.00302 ( 8) SS BOND : angle 2.43848 ( 16) hydrogen bonds : bond 0.03335 ( 508) hydrogen bonds : angle 4.44804 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7121 (mp) cc_final: 0.6801 (mp) REVERT: A 358 TYR cc_start: 0.8293 (m-80) cc_final: 0.8050 (m-80) REVERT: A 372 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8991 (mt) REVERT: B 10 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7918 (mp0) REVERT: E 128 MET cc_start: 0.8560 (mmm) cc_final: 0.7816 (mmm) REVERT: E 234 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8135 (mm-30) REVERT: G 14 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7928 (ptmm) REVERT: G 22 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7714 (tm-30) REVERT: N 34 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (mmm) REVERT: N 82 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7657 (tp40) REVERT: R 38 LYS cc_start: 0.9493 (mtmt) cc_final: 0.9036 (ttmm) REVERT: R 152 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: R 403 CYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8252 (t) REVERT: R 407 ASN cc_start: 0.8540 (t0) cc_final: 0.8147 (t0) outliers start: 26 outliers final: 17 residues processed: 197 average time/residue: 0.1011 time to fit residues: 29.1030 Evaluate side-chains 183 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 113 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.101719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078867 restraints weight = 25449.595| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.73 r_work: 0.3158 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10884 Z= 0.203 Angle : 0.657 10.991 14794 Z= 0.335 Chirality : 0.044 0.185 1641 Planarity : 0.004 0.068 1868 Dihedral : 4.846 49.020 1543 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.70 % Allowed : 15.57 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.03 (0.24), residues: 1328 helix: 1.76 (0.25), residues: 423 sheet: -0.96 (0.26), residues: 363 loop : -0.56 (0.30), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.016 0.002 TYR A 318 PHE 0.017 0.002 PHE E 32 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00464 (10876) covalent geometry : angle 0.65266 (14778) SS BOND : bond 0.00267 ( 8) SS BOND : angle 2.47122 ( 16) hydrogen bonds : bond 0.03634 ( 508) hydrogen bonds : angle 4.53712 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7270 (mp) cc_final: 0.6948 (mp) REVERT: A 358 TYR cc_start: 0.8288 (m-80) cc_final: 0.8055 (m-80) REVERT: A 372 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.9002 (mt) REVERT: B 10 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7870 (mp0) REVERT: E 234 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8196 (mp0) REVERT: G 21 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: G 22 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7919 (tm-30) REVERT: N 82 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7425 (tp40) REVERT: N 117 TYR cc_start: 0.8489 (m-80) cc_final: 0.8143 (m-80) REVERT: R 38 LYS cc_start: 0.9478 (mtmt) cc_final: 0.8954 (ttmm) REVERT: R 152 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: R 195 PHE cc_start: 0.8963 (m-10) cc_final: 0.8750 (m-10) REVERT: R 403 CYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8257 (t) REVERT: R 407 ASN cc_start: 0.8568 (t0) cc_final: 0.8199 (t0) outliers start: 30 outliers final: 21 residues processed: 186 average time/residue: 0.0937 time to fit residues: 25.9244 Evaluate side-chains 182 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081250 restraints weight = 25346.364| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.75 r_work: 0.3205 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10884 Z= 0.123 Angle : 0.632 10.886 14794 Z= 0.318 Chirality : 0.042 0.162 1641 Planarity : 0.004 0.066 1868 Dihedral : 4.667 49.959 1543 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.16 % Allowed : 16.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.24), residues: 1328 helix: 1.80 (0.25), residues: 424 sheet: -0.80 (0.26), residues: 361 loop : -0.54 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.017 0.001 TYR R 88 PHE 0.015 0.001 PHE R 280 TRP 0.016 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 (10876) covalent geometry : angle 0.62824 (14778) SS BOND : bond 0.00265 ( 8) SS BOND : angle 2.21439 ( 16) hydrogen bonds : bond 0.03351 ( 508) hydrogen bonds : angle 4.45114 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7174 (mp) cc_final: 0.6862 (mp) REVERT: A 289 LEU cc_start: 0.9003 (tp) cc_final: 0.8785 (tp) REVERT: A 358 TYR cc_start: 0.8294 (m-80) cc_final: 0.8048 (m-80) REVERT: B 10 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7915 (mp0) REVERT: G 20 LYS cc_start: 0.8823 (mttp) cc_final: 0.8452 (mtmt) REVERT: G 22 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7691 (tm-30) REVERT: N 47 TRP cc_start: 0.8891 (t60) cc_final: 0.8642 (t60) REVERT: N 72 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7422 (ptm160) REVERT: N 82 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7638 (tp40) REVERT: N 87 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8020 (mtmm) REVERT: R 37 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: R 38 LYS cc_start: 0.9458 (mtmt) cc_final: 0.8956 (ttmm) REVERT: R 152 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: R 195 PHE cc_start: 0.8912 (m-10) cc_final: 0.8685 (m-10) REVERT: R 221 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: R 407 ASN cc_start: 0.8548 (t0) cc_final: 0.8171 (t0) outliers start: 24 outliers final: 19 residues processed: 191 average time/residue: 0.0972 time to fit residues: 27.2011 Evaluate side-chains 187 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081233 restraints weight = 25499.075| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.75 r_work: 0.3201 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 10884 Z= 0.215 Angle : 0.931 59.200 14794 Z= 0.521 Chirality : 0.043 0.348 1641 Planarity : 0.004 0.066 1868 Dihedral : 4.679 49.954 1543 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.16 % Allowed : 16.56 % Favored : 81.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.13 (0.24), residues: 1328 helix: 1.78 (0.25), residues: 424 sheet: -0.79 (0.26), residues: 361 loop : -0.54 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.014 0.001 TYR E 178 PHE 0.016 0.001 PHE R 280 TRP 0.015 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00434 (10876) covalent geometry : angle 0.92902 (14778) SS BOND : bond 0.00279 ( 8) SS BOND : angle 2.18792 ( 16) hydrogen bonds : bond 0.03421 ( 508) hydrogen bonds : angle 4.45303 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.75 seconds wall clock time: 44 minutes 26.58 seconds (2666.58 seconds total)