Starting phenix.real_space_refine on Mon Jul 28 18:07:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_22283.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_22283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_22283.map" model { file = "/net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_22283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xox_22283/07_2025/6xox_22283.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} 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: 6.29, per 1000 atoms: 0.59 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: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.27 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: 3.37 Time building geometry restraints manager: 2.80 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: 1.020 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- 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 : 6.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (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 TRP 0.039 0.004 TRP E 111 HIS 0.019 0.003 HIS A 357 PHE 0.038 0.004 PHE E 227 TYR 0.045 0.004 TYR R 242 ARG 0.020 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.11712 ( 508) hydrogen bonds : angle 6.97543 ( 1452) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.60299 ( 16) covalent geometry : bond 0.01107 (10876) covalent geometry : angle 1.10023 (14778) *********************** 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 : 1.087 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: 0.8819 (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: 0.2834 time to fit residues: 105.1308 Evaluate side-chains 165 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 112 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.102026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079463 restraints weight = 25417.121| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.72 r_work: 0.3167 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10884 Z= 0.140 Angle : 0.638 11.559 14794 Z= 0.334 Chirality : 0.044 0.179 1641 Planarity : 0.005 0.064 1868 Dihedral : 5.819 59.353 1550 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.15 % Allowed : 9.00 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1328 helix: 0.02 (0.24), residues: 423 sheet: -1.88 (0.25), residues: 357 loop : -1.40 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.002 PHE R 280 TYR 0.022 0.002 TYR R 148 ARG 0.007 0.001 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 508) hydrogen bonds : angle 5.22483 ( 1452) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.86753 ( 16) covalent geometry : bond 0.00305 (10876) covalent geometry : angle 0.63733 (14778) *********************** 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 255 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 3.052 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8755 (p0) cc_final: 0.8536 (p0) REVERT: A 344 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 386 MET cc_start: 0.8729 (tmm) cc_final: 0.8495 (tmm) REVERT: B 262 MET cc_start: 0.8140 (tpp) cc_final: 0.7769 (ttt) REVERT: E 171 GLN cc_start: 0.8403 (mp10) cc_final: 0.7969 (mp10) REVERT: E 212 VAL cc_start: 0.8122 (t) cc_final: 0.7887 (p) REVERT: N 73 ASP cc_start: 0.7673 (t0) cc_final: 0.7407 (t0) REVERT: N 82 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7477 (tp40) REVERT: N 87 LYS cc_start: 0.9072 (mttt) cc_final: 0.8853 (mtmt) REVERT: N 89 GLU cc_start: 0.8837 (pm20) cc_final: 0.8478 (pm20) REVERT: N 90 ASP cc_start: 0.8360 (m-30) cc_final: 0.7607 (m-30) REVERT: R 272 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8926 (mp) REVERT: R 413 PHE cc_start: 0.7598 (m-80) cc_final: 0.7353 (m-80) outliers start: 35 outliers final: 13 residues processed: 244 average time/residue: 0.2453 time to fit residues: 86.9166 Evaluate side-chains 191 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.101416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078242 restraints weight = 25606.698| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.75 r_work: 0.3143 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10884 Z= 0.178 Angle : 0.624 13.617 14794 Z= 0.324 Chirality : 0.044 0.148 1641 Planarity : 0.004 0.064 1868 Dihedral : 5.253 54.483 1544 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.24 % Allowed : 11.61 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1328 helix: 0.76 (0.25), residues: 423 sheet: -1.78 (0.25), residues: 356 loop : -1.09 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.002 PHE R 413 TYR 0.022 0.002 TYR R 148 ARG 0.004 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 508) hydrogen bonds : angle 4.90798 ( 1452) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.86802 ( 16) covalent geometry : bond 0.00400 (10876) covalent geometry : angle 0.62368 (14778) *********************** 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 229 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7082 (mp) cc_final: 0.6586 (mp) REVERT: A 297 LEU cc_start: 0.7048 (tp) cc_final: 0.6822 (tt) REVERT: A 372 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8930 (mt) REVERT: B 262 MET cc_start: 0.8212 (tpp) cc_final: 0.7804 (ttt) REVERT: E 128 MET cc_start: 0.8466 (mmm) cc_final: 0.8108 (mmm) REVERT: E 171 GLN cc_start: 0.8506 (mp10) cc_final: 0.8046 (mp10) REVERT: G 22 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7910 (tm-30) REVERT: N 89 GLU cc_start: 0.8884 (pm20) cc_final: 0.8684 (pm20) REVERT: N 90 ASP cc_start: 0.8426 (m-30) cc_final: 0.7701 (m-30) REVERT: R 272 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8900 (mp) REVERT: R 413 PHE cc_start: 0.7781 (m-80) cc_final: 0.7490 (m-80) outliers start: 36 outliers final: 19 residues processed: 215 average time/residue: 0.2141 time to fit residues: 66.7606 Evaluate side-chains 184 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 189 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 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 213 GLN A 384 GLN ** 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 130 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 = 0.3689 r_free = 0.3689 target = 0.101779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079164 restraints weight = 25603.743| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.72 r_work: 0.3159 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10884 Z= 0.127 Angle : 0.586 11.179 14794 Z= 0.303 Chirality : 0.042 0.152 1641 Planarity : 0.004 0.065 1868 Dihedral : 4.859 52.690 1544 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.15 % Allowed : 12.69 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1328 helix: 1.28 (0.25), residues: 423 sheet: -1.52 (0.25), residues: 350 loop : -0.85 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 266 PHE 0.014 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 508) hydrogen bonds : angle 4.67122 ( 1452) SS BOND : bond 0.00915 ( 8) SS BOND : angle 1.11635 ( 16) covalent geometry : bond 0.00280 (10876) covalent geometry : angle 0.58529 (14778) *********************** 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 227 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.429 Fit side-chains REVERT: A 56 ILE cc_start: 0.7031 (mp) cc_final: 0.6608 (mp) REVERT: A 372 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8945 (mt) REVERT: B 101 MET cc_start: 0.9233 (mtp) cc_final: 0.8998 (mtp) REVERT: E 128 MET cc_start: 0.8480 (mmm) cc_final: 0.7894 (mmm) REVERT: E 130 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8448 (tp40) REVERT: E 171 GLN cc_start: 0.8529 (mp10) cc_final: 0.8089 (mp10) REVERT: E 234 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8273 (mm-30) REVERT: G 14 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7954 (ptmm) REVERT: G 22 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7891 (tm-30) REVERT: N 90 ASP cc_start: 0.8355 (m-30) cc_final: 0.7701 (m-30) REVERT: R 165 ILE cc_start: 0.8871 (tp) cc_final: 0.8628 (pt) REVERT: R 407 ASN cc_start: 0.8495 (t0) cc_final: 0.8076 (t0) outliers start: 35 outliers final: 18 residues processed: 218 average time/residue: 0.2505 time to fit residues: 80.0053 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 : 1.602 ------------------------------------------------------------------------------- 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 138 GLU 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 130 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 31 optimal weight: 0.0030 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.101509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078900 restraints weight = 25698.144| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.72 r_work: 0.3154 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10884 Z= 0.141 Angle : 0.601 11.788 14794 Z= 0.310 Chirality : 0.043 0.153 1641 Planarity : 0.004 0.064 1868 Dihedral : 4.737 51.274 1543 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.79 % Allowed : 13.95 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1328 helix: 1.51 (0.26), residues: 423 sheet: -1.37 (0.26), residues: 348 loop : -0.73 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 266 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR R 148 ARG 0.007 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 508) hydrogen bonds : angle 4.60320 ( 1452) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.77982 ( 16) covalent geometry : bond 0.00315 (10876) covalent geometry : angle 0.60087 (14778) *********************** 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 210 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7161 (mp) cc_final: 0.6792 (mp) REVERT: A 221 MET cc_start: 0.8267 (ttp) cc_final: 0.8037 (ttm) REVERT: A 372 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8973 (mt) REVERT: B 10 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7893 (mp0) REVERT: B 101 MET cc_start: 0.9251 (mtp) cc_final: 0.9017 (mtp) REVERT: E 128 MET cc_start: 0.8513 (mmm) cc_final: 0.7641 (mmm) REVERT: E 171 GLN cc_start: 0.8436 (mp10) cc_final: 0.8009 (mp10) REVERT: E 206 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7858 (ttp80) REVERT: G 14 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7978 (ptmm) REVERT: G 22 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7846 (tm-30) REVERT: G 32 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8513 (tmtt) REVERT: N 47 TRP cc_start: 0.8909 (t60) cc_final: 0.8705 (t60) REVERT: N 82 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7352 (tp40) REVERT: R 165 ILE cc_start: 0.8860 (tp) cc_final: 0.8629 (pt) REVERT: R 407 ASN cc_start: 0.8525 (t0) cc_final: 0.8116 (t0) outliers start: 31 outliers final: 21 residues processed: 200 average time/residue: 0.2708 time to fit residues: 78.5911 Evaluate side-chains 189 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 138 GLU 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 G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS 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 192 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 104 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.102267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079430 restraints weight = 25669.616| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.76 r_work: 0.3164 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10884 Z= 0.135 Angle : 0.595 10.961 14794 Z= 0.305 Chirality : 0.043 0.164 1641 Planarity : 0.004 0.062 1868 Dihedral : 4.634 50.684 1543 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.25 % Allowed : 15.12 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1328 helix: 1.62 (0.26), residues: 423 sheet: -1.13 (0.26), residues: 361 loop : -0.63 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE A 345 TYR 0.015 0.001 TYR R 148 ARG 0.003 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 508) hydrogen bonds : angle 4.50067 ( 1452) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.75057 ( 16) covalent geometry : bond 0.00303 (10876) covalent geometry : angle 0.59504 (14778) *********************** 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 199 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.349 Fit side-chains REVERT: A 56 ILE cc_start: 0.7183 (mp) cc_final: 0.6858 (mp) REVERT: A 221 MET cc_start: 0.8302 (ttp) cc_final: 0.8088 (ttm) REVERT: A 360 TYR cc_start: 0.9010 (m-80) cc_final: 0.8689 (m-80) REVERT: A 372 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8959 (mt) REVERT: B 10 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7834 (mp0) REVERT: B 101 MET cc_start: 0.9238 (mtp) cc_final: 0.9017 (mtp) REVERT: B 314 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8152 (ptt180) REVERT: E 128 MET cc_start: 0.8512 (mmm) cc_final: 0.7679 (mmm) REVERT: E 206 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7902 (ttp80) REVERT: G 14 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7964 (ptmm) REVERT: G 22 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7810 (tm-30) REVERT: G 32 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8563 (tmtt) REVERT: N 82 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7310 (tp40) REVERT: R 152 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: R 165 ILE cc_start: 0.8848 (tp) cc_final: 0.8630 (pt) REVERT: R 407 ASN cc_start: 0.8584 (t0) cc_final: 0.8282 (t0) REVERT: R 411 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8467 (tt) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.3301 time to fit residues: 91.0773 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 : 2.604 ------------------------------------------------------------------------------- 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 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS 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 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 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 19 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.103835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080864 restraints weight = 25906.432| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.79 r_work: 0.3197 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10884 Z= 0.123 Angle : 0.592 10.671 14794 Z= 0.302 Chirality : 0.042 0.158 1641 Planarity : 0.004 0.063 1868 Dihedral : 4.556 50.317 1543 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.70 % Allowed : 14.85 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1328 helix: 1.76 (0.26), residues: 423 sheet: -0.96 (0.27), residues: 350 loop : -0.58 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE A 345 TYR 0.018 0.001 TYR R 88 ARG 0.003 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 508) hydrogen bonds : angle 4.41442 ( 1452) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.68699 ( 16) covalent geometry : bond 0.00276 (10876) covalent geometry : angle 0.59225 (14778) *********************** 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 210 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7174 (mp) cc_final: 0.6843 (mp) REVERT: A 221 MET cc_start: 0.8255 (ttp) cc_final: 0.8029 (ttm) REVERT: A 348 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7958 (mt) REVERT: B 10 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7835 (mp0) REVERT: B 101 MET cc_start: 0.9237 (mtp) cc_final: 0.9031 (mtp) REVERT: B 198 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8783 (pp) REVERT: E 128 MET cc_start: 0.8440 (mmm) cc_final: 0.7587 (mmm) REVERT: E 206 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7790 (ttp80) REVERT: E 234 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 14 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7925 (ptmm) REVERT: G 22 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7751 (tm-30) REVERT: G 32 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8573 (tmtt) REVERT: N 34 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8588 (mmm) REVERT: N 82 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7463 (tp40) REVERT: R 152 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: R 407 ASN cc_start: 0.8647 (t0) cc_final: 0.8271 (t0) outliers start: 30 outliers final: 21 residues processed: 202 average time/residue: 0.3263 time to fit residues: 96.9272 Evaluate side-chains 186 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 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 G residue 32 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 104 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081808 restraints weight = 25423.538| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.79 r_work: 0.3212 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10884 Z= 0.114 Angle : 0.595 10.287 14794 Z= 0.303 Chirality : 0.042 0.162 1641 Planarity : 0.003 0.065 1868 Dihedral : 4.474 50.039 1543 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.88 % Allowed : 15.39 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1328 helix: 1.89 (0.26), residues: 423 sheet: -0.89 (0.26), residues: 360 loop : -0.55 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE A 345 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 508) hydrogen bonds : angle 4.31289 ( 1452) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.15437 ( 16) covalent geometry : bond 0.00256 (10876) covalent geometry : angle 0.59387 (14778) *********************** 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 212 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8270 (ttp) cc_final: 0.8024 (ttm) REVERT: B 10 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7837 (mp0) REVERT: B 198 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8833 (pp) REVERT: E 206 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7793 (ttp80) REVERT: G 22 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7732 (tm-30) REVERT: G 32 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8556 (tmtt) REVERT: N 34 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: N 82 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7550 (tp40) REVERT: N 117 TYR cc_start: 0.8428 (m-80) cc_final: 0.7931 (m-80) REVERT: R 152 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: R 260 PHE cc_start: 0.7296 (p90) cc_final: 0.6819 (p90) REVERT: R 407 ASN cc_start: 0.8597 (t0) cc_final: 0.8325 (t0) REVERT: R 411 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8503 (tt) outliers start: 32 outliers final: 20 residues processed: 205 average time/residue: 0.2098 time to fit residues: 62.4232 Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 148 TYR 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 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 28 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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** A 387 HIS ** 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 = 0.3737 r_free = 0.3737 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081911 restraints weight = 25494.166| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.78 r_work: 0.3215 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10884 Z= 0.124 Angle : 0.608 10.244 14794 Z= 0.310 Chirality : 0.042 0.165 1641 Planarity : 0.004 0.066 1868 Dihedral : 4.491 49.570 1543 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.52 % Allowed : 15.66 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1328 helix: 1.89 (0.26), residues: 424 sheet: -0.78 (0.26), residues: 366 loop : -0.47 (0.30), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE A 345 TYR 0.017 0.001 TYR R 88 ARG 0.003 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 508) hydrogen bonds : angle 4.33579 ( 1452) SS BOND : bond 0.00304 ( 8) SS BOND : angle 1.02116 ( 16) covalent geometry : bond 0.00279 (10876) covalent geometry : angle 0.60743 (14778) *********************** 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 201 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8290 (ttp) cc_final: 0.8051 (ttm) REVERT: B 10 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7859 (mp0) REVERT: B 198 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8886 (pp) REVERT: B 292 PHE cc_start: 0.8433 (m-10) cc_final: 0.8133 (m-80) REVERT: E 206 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7700 (ttp80) REVERT: G 22 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7713 (tm-30) REVERT: G 32 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8602 (tmtt) REVERT: N 34 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: N 47 TRP cc_start: 0.8872 (t60) cc_final: 0.8644 (t60) REVERT: N 82 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7603 (tp40) REVERT: R 152 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: R 260 PHE cc_start: 0.7205 (p90) cc_final: 0.6731 (p90) REVERT: R 407 ASN cc_start: 0.8615 (t0) cc_final: 0.8337 (t0) REVERT: R 411 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (tt) outliers start: 28 outliers final: 20 residues processed: 194 average time/residue: 0.2205 time to fit residues: 61.6254 Evaluate side-chains 186 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 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 G residue 32 LYS Chi-restraints excluded: chain N residue 34 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 192 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 61 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080812 restraints weight = 25488.097| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.75 r_work: 0.3194 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10884 Z= 0.148 Angle : 0.634 11.958 14794 Z= 0.321 Chirality : 0.043 0.175 1641 Planarity : 0.004 0.067 1868 Dihedral : 4.534 49.253 1543 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.52 % Allowed : 15.12 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1328 helix: 1.89 (0.26), residues: 424 sheet: -0.74 (0.26), residues: 364 loop : -0.46 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE A 345 TYR 0.017 0.001 TYR N 60 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 508) hydrogen bonds : angle 4.36567 ( 1452) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.11870 ( 16) covalent geometry : bond 0.00340 (10876) covalent geometry : angle 0.63294 (14778) ********************** 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 189 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8287 (ttp) cc_final: 0.8046 (ttm) REVERT: B 10 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7866 (mp0) REVERT: E 180 MET cc_start: 0.8320 (ptm) cc_final: 0.8115 (ptm) REVERT: E 206 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7676 (ttp80) REVERT: E 234 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8076 (mp0) REVERT: G 22 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7831 (tm-30) REVERT: G 32 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (tmtt) REVERT: N 34 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8488 (mmm) REVERT: N 60 TYR cc_start: 0.8757 (m-80) cc_final: 0.8469 (m-80) REVERT: N 73 ASP cc_start: 0.7631 (t0) cc_final: 0.7395 (t0) REVERT: N 80 TYR cc_start: 0.7970 (m-80) cc_final: 0.7665 (m-80) REVERT: N 82 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7508 (tp40) REVERT: N 110 VAL cc_start: 0.8841 (t) cc_final: 0.8630 (p) REVERT: N 117 TYR cc_start: 0.8461 (m-80) cc_final: 0.8062 (m-80) REVERT: R 152 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: R 260 PHE cc_start: 0.7198 (p90) cc_final: 0.6741 (p90) REVERT: R 407 ASN cc_start: 0.8622 (t0) cc_final: 0.8358 (t0) REVERT: R 411 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 28 outliers final: 23 residues processed: 182 average time/residue: 0.2252 time to fit residues: 59.3682 Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 138 GLU 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 G residue 32 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 148 TYR 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 224 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 0.0470 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.103942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080999 restraints weight = 25415.427| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.76 r_work: 0.3196 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3598 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= 0.139 Angle : 0.629 11.633 14794 Z= 0.317 Chirality : 0.043 0.172 1641 Planarity : 0.004 0.066 1868 Dihedral : 4.526 49.368 1543 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 15.30 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1328 helix: 1.88 (0.26), residues: 424 sheet: -0.67 (0.26), residues: 364 loop : -0.45 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE A 345 TYR 0.017 0.001 TYR R 88 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 508) hydrogen bonds : angle 4.34655 ( 1452) SS BOND : bond 0.00288 ( 8) SS BOND : angle 1.03122 ( 16) covalent geometry : bond 0.00316 (10876) covalent geometry : angle 0.62806 (14778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5842.44 seconds wall clock time: 107 minutes 18.11 seconds (6438.11 seconds total)