Starting phenix.real_space_refine on Thu Jul 2 13:31:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vau_64905/07_2026/9vau_64905.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5591 2.51 5 N 1504 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8782 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2243 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1772 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8782 At special positions: 0 Unit cell: (121.9, 117.66, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1627 8.00 N 1504 7.00 C 5591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.15 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: 0.73 Conformation dependent library (CDL) restraints added in 477.0 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 59 through 89 Processing helix chain 'R' and resid 99 through 127 removed outlier: 3.597A pdb=" N ALA R 119 " --> pdb=" O THR R 115 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 206 Proline residue: R 202 - end of helix removed outlier: 3.804A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 269 Processing helix chain 'R' and resid 293 through 329 removed outlier: 3.533A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 363 removed outlier: 3.563A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.504A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.971A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.948A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.644A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.675A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.266A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 8.932A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.636A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.592A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.007A 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: 3.511A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.697A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.759A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.129A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.279A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.336A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1909 1.33 - 1.47: 3168 1.47 - 1.60: 3802 1.60 - 1.74: 0 1.74 - 1.88: 88 Bond restraints: 8967 Sorted by residual: bond pdb=" CA SER D 53 " pdb=" CB SER D 53 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.64e-02 3.72e+03 2.25e+01 bond pdb=" CA ALA B 60 " pdb=" CB ALA B 60 " ideal model delta sigma weight residual 1.534 1.462 0.072 1.78e-02 3.16e+03 1.62e+01 bond pdb=" CG HIS B 54 " pdb=" CD2 HIS B 54 " ideal model delta sigma weight residual 1.354 1.310 0.044 1.10e-02 8.26e+03 1.61e+01 bond pdb=" CD2 HIS D 35 " pdb=" NE2 HIS D 35 " ideal model delta sigma weight residual 1.374 1.418 -0.044 1.10e-02 8.26e+03 1.61e+01 bond pdb=" CG HIS B 62 " pdb=" CD2 HIS B 62 " ideal model delta sigma weight residual 1.354 1.310 0.044 1.10e-02 8.26e+03 1.57e+01 ... (remaining 8962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 9573 2.01 - 4.01: 2241 4.01 - 6.02: 300 6.02 - 8.02: 35 8.02 - 10.03: 6 Bond angle restraints: 12155 Sorted by residual: angle pdb=" C LYS A 46 " pdb=" CA LYS A 46 " pdb=" CB LYS A 46 " ideal model delta sigma weight residual 110.88 101.48 9.40 1.57e+00 4.06e-01 3.58e+01 angle pdb=" N LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta sigma weight residual 110.99 100.96 10.03 1.77e+00 3.19e-01 3.21e+01 angle pdb=" CA PHE R 345 " pdb=" CB PHE R 345 " pdb=" CG PHE R 345 " ideal model delta sigma weight residual 113.80 119.25 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" CB HIS B 54 " pdb=" CG HIS B 54 " pdb=" CD2 HIS B 54 " ideal model delta sigma weight residual 131.20 124.33 6.87 1.30e+00 5.92e-01 2.79e+01 angle pdb=" C THR B 329 " pdb=" CA THR B 329 " pdb=" CB THR B 329 " ideal model delta sigma weight residual 110.14 102.63 7.51 1.54e+00 4.22e-01 2.38e+01 ... (remaining 12150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 5123 25.96 - 51.92: 164 51.92 - 77.89: 13 77.89 - 103.85: 2 103.85 - 129.81: 1 Dihedral angle restraints: 5303 sinusoidal: 2029 harmonic: 3274 Sorted by residual: dihedral pdb=" CA TYR D 223 " pdb=" C TYR D 223 " pdb=" N PRO D 224 " pdb=" CA PRO D 224 " ideal model delta harmonic sigma weight residual 180.00 50.19 129.81 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 -177.46 -89.54 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 693 0.063 - 0.125: 454 0.125 - 0.188: 194 0.188 - 0.250: 38 0.250 - 0.313: 10 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA ARG B 22 " pdb=" N ARG B 22 " pdb=" C ARG B 22 " pdb=" CB ARG B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA SER B 331 " pdb=" N SER B 331 " pdb=" C SER B 331 " pdb=" CB SER B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1386 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.026 2.00e-02 2.50e+03 3.85e-02 3.70e+01 pdb=" CG TRP B 63 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 212 " -0.025 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP A 212 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 212 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 212 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 212 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 212 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 212 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 212 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 212 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP A 212 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 111 " -0.020 2.00e-02 2.50e+03 3.44e-02 2.95e+01 pdb=" CG TRP D 111 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 111 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 111 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP D 111 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP D 111 " -0.060 2.00e-02 2.50e+03 pdb=" CE3 TRP D 111 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 111 " 0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP D 111 " 0.018 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1776 2.80 - 3.33: 8893 3.33 - 3.85: 15127 3.85 - 4.38: 18556 4.38 - 4.90: 30127 Nonbonded interactions: 74479 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU R 123 " pdb=" OH TYR R 354 " model vdw 2.331 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.378 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.424 3.040 ... (remaining 74474 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: 0.230 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 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 0.114 8969 Z= 0.691 Angle : 1.700 10.028 12159 Z= 1.137 Chirality : 0.091 0.313 1389 Planarity : 0.012 0.138 1533 Dihedral : 12.758 129.812 3187 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 1.26 % Allowed : 6.11 % Favored : 92.62 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1108 helix: -1.10 (0.22), residues: 393 sheet: -0.65 (0.30), residues: 271 loop : -1.58 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.005 ARG R 268 TYR 0.086 0.013 TYR B 289 PHE 0.058 0.012 PHE D 165 TRP 0.062 0.019 TRP B 63 HIS 0.025 0.006 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.69 ( 8967) covalent geometry : angle 1.69776 / 1.14 (12155) SS BOND : bond 0.08116 / 3.87 ( 2) SS BOND : angle 5.30316 / 2.83 ( 4) hydrogen bonds : bond 0.20203 / 13.85 ( 474) hydrogen bonds : angle 7.63173 / 5.58 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: R 60 ILE cc_start: 0.9026 (pt) cc_final: 0.8781 (tp) REVERT: R 63 LYS cc_start: 0.8603 (mttt) cc_final: 0.8397 (mtmm) REVERT: R 70 TYR cc_start: 0.9105 (m-10) cc_final: 0.8761 (m-80) REVERT: R 112 ASP cc_start: 0.9307 (m-30) cc_final: 0.9090 (t0) REVERT: R 126 ASN cc_start: 0.9561 (m-40) cc_final: 0.8655 (m-40) REVERT: R 129 TRP cc_start: 0.8108 (m100) cc_final: 0.7796 (m100) REVERT: R 134 TRP cc_start: 0.8966 (t-100) cc_final: 0.8541 (t-100) REVERT: R 171 CYS cc_start: 0.8307 (m) cc_final: 0.8065 (t) REVERT: R 187 LYS cc_start: 0.9300 (mttt) cc_final: 0.8907 (tttt) REVERT: R 210 GLN cc_start: 0.8895 (tt0) cc_final: 0.8487 (tt0) REVERT: R 296 GLN cc_start: 0.9219 (mm110) cc_final: 0.8804 (mp10) REVERT: R 333 GLN cc_start: 0.8190 (mt0) cc_final: 0.7603 (tp-100) REVERT: R 357 SER cc_start: 0.9329 (m) cc_final: 0.8284 (t) REVERT: A 333 GLN cc_start: 0.9047 (tp40) cc_final: 0.8746 (tp-100) REVERT: B 217 MET cc_start: 0.8701 (mtm) cc_final: 0.8422 (ptt) REVERT: C 17 GLU cc_start: 0.9734 (tp30) cc_final: 0.9477 (tp30) outliers start: 12 outliers final: 0 residues processed: 191 average time/residue: 0.7506 time to fit residues: 150.4268 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 269 GLN R 343 HIS R 350 ASN A 205 GLN A 214 HIS B 9 GLN B 91 HIS B 176 GLN B 239 ASN B 259 GLN C 18 GLN D 174 GLN D 182 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050034 restraints weight = 22789.165| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.11 r_work: 0.2533 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8969 Z= 0.205 Angle : 0.626 7.653 12159 Z= 0.338 Chirality : 0.044 0.147 1389 Planarity : 0.004 0.070 1533 Dihedral : 4.881 67.260 1222 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Rotamer: Outliers : 2.11 % Allowed : 12.75 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1108 helix: 1.70 (0.24), residues: 397 sheet: -0.09 (0.31), residues: 275 loop : -0.88 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.021 0.002 TYR A 297 PHE 0.014 0.002 PHE R 312 TRP 0.025 0.002 TRP B 211 HIS 0.007 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 8967) covalent geometry : angle 0.62553 / 0.34 (12155) SS BOND : bond 0.00757 / 0.37 ( 2) SS BOND : angle 2.00107 / 0.98 ( 4) hydrogen bonds : bond 0.05185 / 3.45 ( 474) hydrogen bonds : angle 5.16231 / 3.81 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8522 (mttt) cc_final: 0.8169 (mtmm) REVERT: R 126 ASN cc_start: 0.9197 (m-40) cc_final: 0.8394 (m-40) REVERT: R 129 TRP cc_start: 0.8285 (m100) cc_final: 0.8051 (m100) REVERT: R 187 LYS cc_start: 0.8740 (mttt) cc_final: 0.8348 (tttt) REVERT: R 296 GLN cc_start: 0.8679 (mm110) cc_final: 0.8282 (mp10) REVERT: R 333 GLN cc_start: 0.8239 (mt0) cc_final: 0.7566 (tp40) REVERT: A 189 HIS cc_start: 0.8069 (m90) cc_final: 0.7742 (m90) REVERT: A 208 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 233 GLN cc_start: 0.8711 (mt0) cc_final: 0.8326 (mt0) REVERT: A 243 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8574 (tpp80) REVERT: A 333 GLN cc_start: 0.8658 (tp40) cc_final: 0.8163 (tp-100) REVERT: B 10 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 130 GLU cc_start: 0.9187 (mp0) cc_final: 0.8968 (mp0) REVERT: B 217 MET cc_start: 0.8114 (mtm) cc_final: 0.7627 (ptt) REVERT: B 249 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8517 (p) REVERT: C 17 GLU cc_start: 0.9417 (tp30) cc_final: 0.9078 (mm-30) REVERT: C 20 LYS cc_start: 0.8741 (mtmp) cc_final: 0.7772 (mtmm) REVERT: C 28 ILE cc_start: 0.9144 (pt) cc_final: 0.8794 (pp) REVERT: C 29 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (mmmm) REVERT: C 58 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8823 (pm20) REVERT: D 46 GLU cc_start: 0.8756 (tt0) cc_final: 0.8329 (tt0) REVERT: D 204 ILE cc_start: 0.9151 (mt) cc_final: 0.8499 (pp) REVERT: D 211 ASP cc_start: 0.8618 (m-30) cc_final: 0.8230 (m-30) outliers start: 20 outliers final: 6 residues processed: 158 average time/residue: 0.6186 time to fit residues: 102.8636 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 29 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 269 GLN A 205 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047748 restraints weight = 23031.815| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.10 r_work: 0.2486 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8969 Z= 0.263 Angle : 0.624 7.558 12159 Z= 0.334 Chirality : 0.044 0.219 1389 Planarity : 0.004 0.068 1533 Dihedral : 4.735 66.181 1222 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 13.80 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1108 helix: 2.10 (0.25), residues: 396 sheet: 0.08 (0.31), residues: 283 loop : -0.79 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.023 0.002 TYR R 70 PHE 0.019 0.002 PHE R 312 TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 ( 8967) covalent geometry : angle 0.62263 / 0.33 (12155) SS BOND : bond 0.00859 / 0.42 ( 2) SS BOND : angle 1.95646 / 0.93 ( 4) hydrogen bonds : bond 0.05211 / 3.53 ( 474) hydrogen bonds : angle 5.00630 / 3.69 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8833 (mttt) cc_final: 0.8437 (mtmm) REVERT: R 112 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8698 (t0) REVERT: R 126 ASN cc_start: 0.9167 (m-40) cc_final: 0.8622 (m-40) REVERT: R 129 TRP cc_start: 0.8316 (m100) cc_final: 0.8013 (m100) REVERT: R 187 LYS cc_start: 0.8809 (mttt) cc_final: 0.8340 (tttt) REVERT: R 296 GLN cc_start: 0.8740 (mm110) cc_final: 0.8433 (mp10) REVERT: R 333 GLN cc_start: 0.8246 (mt0) cc_final: 0.7674 (tp40) REVERT: R 334 TRP cc_start: 0.7517 (m100) cc_final: 0.7313 (m100) REVERT: R 354 TYR cc_start: 0.8685 (m-80) cc_final: 0.8329 (m-80) REVERT: A 189 HIS cc_start: 0.8331 (m90) cc_final: 0.8054 (m90) REVERT: A 206 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8401 (mmm-85) REVERT: A 208 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: A 233 GLN cc_start: 0.8685 (mt0) cc_final: 0.8350 (mt0) REVERT: A 333 GLN cc_start: 0.8774 (tp40) cc_final: 0.8353 (tp40) REVERT: B 10 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 217 MET cc_start: 0.8250 (mtm) cc_final: 0.7764 (ptt) REVERT: B 249 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 325 MET cc_start: 0.9265 (tpt) cc_final: 0.8781 (tpp) REVERT: B 340 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8569 (t0) REVERT: C 17 GLU cc_start: 0.9401 (tp30) cc_final: 0.9098 (mm-30) REVERT: C 20 LYS cc_start: 0.8685 (mtmp) cc_final: 0.7915 (mttm) REVERT: C 28 ILE cc_start: 0.9181 (pt) cc_final: 0.8401 (pp) REVERT: C 29 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8055 (mttm) REVERT: C 58 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8925 (mp0) REVERT: D 46 GLU cc_start: 0.8806 (tt0) cc_final: 0.8307 (tt0) REVERT: D 208 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 211 ASP cc_start: 0.8660 (m-30) cc_final: 0.7614 (m-30) outliers start: 30 outliers final: 9 residues processed: 142 average time/residue: 0.7255 time to fit residues: 108.3803 Evaluate side-chains 127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.049008 restraints weight = 23444.344| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.19 r_work: 0.2514 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8969 Z= 0.172 Angle : 0.566 7.523 12159 Z= 0.302 Chirality : 0.042 0.291 1389 Planarity : 0.004 0.061 1533 Dihedral : 4.492 59.585 1222 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.48 % Allowed : 12.96 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1108 helix: 2.28 (0.25), residues: 402 sheet: 0.18 (0.31), residues: 270 loop : -0.67 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.014 0.001 TYR A 297 PHE 0.015 0.001 PHE R 312 TRP 0.020 0.002 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8967) covalent geometry : angle 0.56554 / 0.30 (12155) SS BOND : bond 0.00656 / 0.32 ( 2) SS BOND : angle 1.29800 / 0.61 ( 4) hydrogen bonds : bond 0.04517 / 3.05 ( 474) hydrogen bonds : angle 4.74372 / 3.49 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8815 (mttt) cc_final: 0.8443 (mtmm) REVERT: R 112 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8660 (t0) REVERT: R 126 ASN cc_start: 0.9170 (m-40) cc_final: 0.8530 (m-40) REVERT: R 129 TRP cc_start: 0.8333 (m100) cc_final: 0.8042 (m100) REVERT: R 187 LYS cc_start: 0.8802 (mttt) cc_final: 0.8293 (tttt) REVERT: R 296 GLN cc_start: 0.8815 (mm110) cc_final: 0.8494 (mp10) REVERT: R 333 GLN cc_start: 0.8210 (mt0) cc_final: 0.7787 (tp40) REVERT: R 334 TRP cc_start: 0.7401 (m100) cc_final: 0.7180 (m100) REVERT: R 354 TYR cc_start: 0.8472 (m-80) cc_final: 0.8246 (m-80) REVERT: A 189 HIS cc_start: 0.8258 (m90) cc_final: 0.7947 (m90) REVERT: A 206 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8447 (mmm-85) REVERT: A 208 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7596 (tp30) REVERT: A 233 GLN cc_start: 0.8757 (mt0) cc_final: 0.8438 (mt0) REVERT: A 307 GLN cc_start: 0.9520 (mm-40) cc_final: 0.9199 (mm-40) REVERT: A 333 GLN cc_start: 0.8744 (tp40) cc_final: 0.8211 (tp-100) REVERT: B 10 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8608 (mm-30) REVERT: B 217 MET cc_start: 0.8175 (mtm) cc_final: 0.7759 (ptt) REVERT: B 249 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 325 MET cc_start: 0.9231 (tpt) cc_final: 0.8983 (tpp) REVERT: C 17 GLU cc_start: 0.9410 (tp30) cc_final: 0.9129 (mm-30) REVERT: C 20 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7909 (mttm) REVERT: C 29 LYS cc_start: 0.8216 (mtpp) cc_final: 0.8005 (mmmm) REVERT: C 58 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8739 (pm20) REVERT: D 46 GLU cc_start: 0.8763 (tt0) cc_final: 0.8313 (tt0) REVERT: D 132 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8191 (p) REVERT: D 206 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8848 (mtm-85) REVERT: D 208 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 211 ASP cc_start: 0.8597 (m-30) cc_final: 0.8255 (m-30) outliers start: 33 outliers final: 13 residues processed: 140 average time/residue: 0.7233 time to fit residues: 106.6026 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 210 GLN R 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.049561 restraints weight = 23415.550| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.12 r_work: 0.2531 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8969 Z= 0.154 Angle : 0.559 9.654 12159 Z= 0.294 Chirality : 0.042 0.300 1389 Planarity : 0.004 0.062 1533 Dihedral : 4.314 56.322 1222 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.37 % Allowed : 13.49 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1108 helix: 2.42 (0.26), residues: 404 sheet: 0.17 (0.31), residues: 270 loop : -0.65 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 206 TYR 0.013 0.001 TYR D 178 PHE 0.012 0.001 PHE R 312 TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8967) covalent geometry : angle 0.55880 / 0.29 (12155) SS BOND : bond 0.00531 / 0.26 ( 2) SS BOND : angle 0.98899 / 0.49 ( 4) hydrogen bonds : bond 0.04237 / 2.85 ( 474) hydrogen bonds : angle 4.64306 / 3.42 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.417 Fit side-chains REVERT: R 63 LYS cc_start: 0.8808 (mttt) cc_final: 0.8425 (mtmm) REVERT: R 112 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8610 (t0) REVERT: R 126 ASN cc_start: 0.9175 (m-40) cc_final: 0.8545 (m-40) REVERT: R 129 TRP cc_start: 0.8374 (m100) cc_final: 0.7996 (m100) REVERT: R 187 LYS cc_start: 0.8801 (mttt) cc_final: 0.8301 (tttt) REVERT: R 296 GLN cc_start: 0.8798 (mm110) cc_final: 0.8477 (mp10) REVERT: R 333 GLN cc_start: 0.8249 (mt0) cc_final: 0.7830 (tp40) REVERT: R 334 TRP cc_start: 0.7534 (m100) cc_final: 0.7194 (m100) REVERT: R 354 TYR cc_start: 0.8426 (m-80) cc_final: 0.8154 (m-80) REVERT: A 189 HIS cc_start: 0.8295 (m90) cc_final: 0.7935 (m90) REVERT: A 206 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8536 (mmm-85) REVERT: A 233 GLN cc_start: 0.8794 (mt0) cc_final: 0.8413 (mt0) REVERT: A 243 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8540 (tpp80) REVERT: A 307 GLN cc_start: 0.9540 (mm-40) cc_final: 0.9209 (mp-120) REVERT: A 333 GLN cc_start: 0.8774 (tp40) cc_final: 0.8213 (tp-100) REVERT: B 8 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8287 (mtm110) REVERT: B 10 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8597 (mm-30) REVERT: B 217 MET cc_start: 0.8186 (mtm) cc_final: 0.7805 (ptt) REVERT: B 249 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (p) REVERT: B 254 ASP cc_start: 0.8442 (t70) cc_final: 0.8076 (t0) REVERT: B 325 MET cc_start: 0.9172 (tpt) cc_final: 0.8871 (tpp) REVERT: C 17 GLU cc_start: 0.9411 (tp30) cc_final: 0.9073 (mm-30) REVERT: C 20 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: C 24 ASN cc_start: 0.8915 (m110) cc_final: 0.8695 (m110) REVERT: C 58 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8782 (pm20) REVERT: D 46 GLU cc_start: 0.8671 (tt0) cc_final: 0.8196 (tt0) REVERT: D 87 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7130 (mtm-85) REVERT: D 132 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8248 (p) REVERT: D 206 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8912 (mtm-85) REVERT: D 208 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 210 GLU cc_start: 0.8317 (pm20) cc_final: 0.7774 (pp20) REVERT: D 211 ASP cc_start: 0.8535 (m-30) cc_final: 0.8160 (m-30) REVERT: D 218 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9090 (ttp) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 0.7404 time to fit residues: 107.5591 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 210 GLN R 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.049391 restraints weight = 23412.704| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.11 r_work: 0.2528 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8969 Z= 0.168 Angle : 0.563 8.741 12159 Z= 0.296 Chirality : 0.042 0.327 1389 Planarity : 0.004 0.061 1533 Dihedral : 4.314 55.542 1222 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.37 % Allowed : 14.96 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1108 helix: 2.43 (0.26), residues: 404 sheet: 0.11 (0.30), residues: 282 loop : -0.62 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 206 TYR 0.013 0.001 TYR D 178 PHE 0.011 0.001 PHE R 312 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8967) covalent geometry : angle 0.56318 / 0.30 (12155) SS BOND : bond 0.00606 / 0.30 ( 2) SS BOND : angle 1.17747 / 0.57 ( 4) hydrogen bonds : bond 0.04270 / 2.88 ( 474) hydrogen bonds : angle 4.63653 / 3.42 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.386 Fit side-chains REVERT: R 63 LYS cc_start: 0.8814 (mttt) cc_final: 0.8484 (mtmm) REVERT: R 112 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8615 (t0) REVERT: R 126 ASN cc_start: 0.9181 (m-40) cc_final: 0.8525 (m-40) REVERT: R 129 TRP cc_start: 0.8379 (m100) cc_final: 0.8045 (m100) REVERT: R 187 LYS cc_start: 0.8808 (mttt) cc_final: 0.8298 (tttt) REVERT: R 210 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8148 (pp30) REVERT: R 296 GLN cc_start: 0.8859 (mm110) cc_final: 0.8506 (mp10) REVERT: R 333 GLN cc_start: 0.8275 (mt0) cc_final: 0.7864 (tp40) REVERT: R 334 TRP cc_start: 0.7594 (m100) cc_final: 0.7184 (m100) REVERT: R 354 TYR cc_start: 0.8435 (m-80) cc_final: 0.8134 (m-80) REVERT: A 189 HIS cc_start: 0.8324 (m90) cc_final: 0.7945 (m90) REVERT: A 233 GLN cc_start: 0.8857 (mt0) cc_final: 0.8479 (mt0) REVERT: A 307 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9195 (mp-120) REVERT: A 333 GLN cc_start: 0.8760 (tp40) cc_final: 0.7794 (tp-100) REVERT: B 8 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8345 (mtm110) REVERT: B 10 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 130 GLU cc_start: 0.9092 (mp0) cc_final: 0.8866 (mp0) REVERT: B 217 MET cc_start: 0.8195 (mtm) cc_final: 0.7798 (ptt) REVERT: B 249 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 254 ASP cc_start: 0.8418 (t70) cc_final: 0.8047 (t0) REVERT: C 17 GLU cc_start: 0.9412 (tp30) cc_final: 0.9073 (mm-30) REVERT: C 20 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7714 (mtmm) REVERT: C 24 ASN cc_start: 0.8917 (m110) cc_final: 0.8664 (m110) REVERT: C 58 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8759 (pm20) REVERT: D 46 GLU cc_start: 0.8686 (tt0) cc_final: 0.8220 (tt0) REVERT: D 87 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7159 (mtm-85) REVERT: D 132 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8290 (p) REVERT: D 206 ARG cc_start: 0.9143 (mtm-85) cc_final: 0.8785 (mpp-170) REVERT: D 208 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7465 (mm-30) REVERT: D 210 GLU cc_start: 0.8335 (pm20) cc_final: 0.7785 (pp20) REVERT: D 211 ASP cc_start: 0.8514 (m-30) cc_final: 0.8167 (m-30) outliers start: 32 outliers final: 15 residues processed: 135 average time/residue: 0.7277 time to fit residues: 103.3365 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 347 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.049560 restraints weight = 23639.548| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.14 r_work: 0.2535 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8969 Z= 0.155 Angle : 0.561 8.842 12159 Z= 0.293 Chirality : 0.041 0.135 1389 Planarity : 0.004 0.062 1533 Dihedral : 4.232 54.786 1222 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.95 % Allowed : 15.60 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1108 helix: 2.52 (0.26), residues: 404 sheet: 0.13 (0.30), residues: 287 loop : -0.53 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 243 TYR 0.013 0.001 TYR D 178 PHE 0.011 0.001 PHE B 253 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8967) covalent geometry : angle 0.56117 / 0.29 (12155) SS BOND : bond 0.00623 / 0.31 ( 2) SS BOND : angle 1.05638 / 0.52 ( 4) hydrogen bonds : bond 0.04126 / 2.79 ( 474) hydrogen bonds : angle 4.58791 / 3.39 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8812 (mttt) cc_final: 0.8478 (mtmm) REVERT: R 112 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (t0) REVERT: R 123 GLU cc_start: 0.8998 (tt0) cc_final: 0.8668 (mt-10) REVERT: R 129 TRP cc_start: 0.8340 (m100) cc_final: 0.8015 (m100) REVERT: R 187 LYS cc_start: 0.8806 (mttt) cc_final: 0.8288 (tmtt) REVERT: R 296 GLN cc_start: 0.8843 (mm110) cc_final: 0.8541 (mp10) REVERT: R 300 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5903 (t-90) REVERT: R 333 GLN cc_start: 0.8354 (mt0) cc_final: 0.7947 (tp40) REVERT: R 334 TRP cc_start: 0.7618 (m100) cc_final: 0.7180 (m100) REVERT: R 354 TYR cc_start: 0.8476 (m-80) cc_final: 0.8163 (m-80) REVERT: A 189 HIS cc_start: 0.8324 (m90) cc_final: 0.7936 (m90) REVERT: A 233 GLN cc_start: 0.8882 (mt0) cc_final: 0.8581 (mt0) REVERT: A 307 GLN cc_start: 0.9538 (mm-40) cc_final: 0.9182 (mp-120) REVERT: A 333 GLN cc_start: 0.8726 (tp40) cc_final: 0.8188 (tp-100) REVERT: B 10 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 130 GLU cc_start: 0.9096 (mp0) cc_final: 0.8853 (mp0) REVERT: B 217 MET cc_start: 0.8169 (mtm) cc_final: 0.7800 (ptt) REVERT: B 249 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 254 ASP cc_start: 0.8415 (t70) cc_final: 0.8050 (t0) REVERT: B 325 MET cc_start: 0.9215 (tpt) cc_final: 0.8933 (tpp) REVERT: C 17 GLU cc_start: 0.9412 (tp30) cc_final: 0.9104 (mm-30) REVERT: C 20 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7785 (mtmm) REVERT: C 24 ASN cc_start: 0.8888 (m110) cc_final: 0.8626 (m110) REVERT: C 58 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8792 (pm20) REVERT: D 46 GLU cc_start: 0.8679 (tt0) cc_final: 0.8191 (tt0) REVERT: D 87 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7223 (mtm-85) REVERT: D 132 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8319 (p) REVERT: D 206 ARG cc_start: 0.9070 (mtm-85) cc_final: 0.8762 (mtm-85) REVERT: D 208 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7383 (mm-30) REVERT: D 210 GLU cc_start: 0.8383 (pm20) cc_final: 0.7811 (pp20) REVERT: D 211 ASP cc_start: 0.8560 (m-30) cc_final: 0.8052 (m-30) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 0.7128 time to fit residues: 106.6890 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 347 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.049971 restraints weight = 23317.593| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.11 r_work: 0.2540 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8969 Z= 0.154 Angle : 0.582 10.258 12159 Z= 0.301 Chirality : 0.042 0.360 1389 Planarity : 0.004 0.062 1533 Dihedral : 4.204 54.971 1222 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.06 % Allowed : 15.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1108 helix: 2.58 (0.26), residues: 404 sheet: 0.15 (0.30), residues: 286 loop : -0.51 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 243 TYR 0.012 0.001 TYR D 178 PHE 0.011 0.001 PHE B 253 TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8967) covalent geometry : angle 0.58224 / 0.30 (12155) SS BOND : bond 0.00569 / 0.28 ( 2) SS BOND : angle 0.92780 / 0.44 ( 4) hydrogen bonds : bond 0.04057 / 2.74 ( 474) hydrogen bonds : angle 4.58534 / 3.41 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8837 (mttt) cc_final: 0.8504 (mtmm) REVERT: R 112 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8631 (t0) REVERT: R 129 TRP cc_start: 0.8410 (m100) cc_final: 0.8055 (m100) REVERT: R 187 LYS cc_start: 0.8813 (mttt) cc_final: 0.8220 (tmtt) REVERT: R 296 GLN cc_start: 0.8861 (mm110) cc_final: 0.8534 (mp10) REVERT: R 300 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5884 (t-90) REVERT: R 333 GLN cc_start: 0.8371 (mt0) cc_final: 0.7992 (tp40) REVERT: R 334 TRP cc_start: 0.7641 (m100) cc_final: 0.7175 (m100) REVERT: R 354 TYR cc_start: 0.8511 (m-80) cc_final: 0.8210 (m-80) REVERT: A 189 HIS cc_start: 0.8285 (m90) cc_final: 0.7886 (m90) REVERT: A 233 GLN cc_start: 0.8861 (mt0) cc_final: 0.8492 (mt0) REVERT: A 307 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9226 (mp-120) REVERT: A 313 ARG cc_start: 0.8877 (mtm-85) cc_final: 0.8553 (mtt180) REVERT: A 333 GLN cc_start: 0.8740 (tp40) cc_final: 0.8223 (tp-100) REVERT: B 10 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 130 GLU cc_start: 0.9128 (mp0) cc_final: 0.8856 (mp0) REVERT: B 217 MET cc_start: 0.8192 (mtm) cc_final: 0.7894 (ptt) REVERT: B 249 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 254 ASP cc_start: 0.8442 (t70) cc_final: 0.8083 (t0) REVERT: B 325 MET cc_start: 0.9255 (tpt) cc_final: 0.8992 (tpp) REVERT: C 17 GLU cc_start: 0.9414 (tp30) cc_final: 0.9092 (mm-30) REVERT: C 20 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7701 (mtmm) REVERT: C 24 ASN cc_start: 0.8897 (m110) cc_final: 0.8637 (m110) REVERT: C 58 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8816 (pm20) REVERT: D 46 GLU cc_start: 0.8685 (tt0) cc_final: 0.8198 (tt0) REVERT: D 132 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8327 (p) REVERT: D 206 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8855 (mtm-85) REVERT: D 208 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 210 GLU cc_start: 0.8387 (pm20) cc_final: 0.7825 (pp20) REVERT: D 211 ASP cc_start: 0.8551 (m-30) cc_final: 0.8094 (m-30) outliers start: 29 outliers final: 15 residues processed: 139 average time/residue: 0.7199 time to fit residues: 105.4865 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 347 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN A 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.066924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.047921 restraints weight = 23640.731| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.14 r_work: 0.2483 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8969 Z= 0.268 Angle : 0.650 10.615 12159 Z= 0.338 Chirality : 0.044 0.141 1389 Planarity : 0.004 0.065 1533 Dihedral : 4.484 58.084 1222 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 15.91 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1108 helix: 2.32 (0.26), residues: 398 sheet: 0.09 (0.29), residues: 297 loop : -0.62 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.014 0.001 TYR D 178 PHE 0.012 0.002 PHE B 253 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 ( 8967) covalent geometry : angle 0.64951 / 0.34 (12155) SS BOND : bond 0.00748 / 0.37 ( 2) SS BOND : angle 1.10299 / 0.51 ( 4) hydrogen bonds : bond 0.04737 / 3.20 ( 474) hydrogen bonds : angle 4.82688 / 3.59 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8806 (mttt) cc_final: 0.8484 (mtmm) REVERT: R 112 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8638 (t0) REVERT: R 129 TRP cc_start: 0.8343 (m100) cc_final: 0.8019 (m100) REVERT: R 187 LYS cc_start: 0.8838 (mttt) cc_final: 0.8304 (tttt) REVERT: R 207 MET cc_start: 0.8774 (mmm) cc_final: 0.8530 (tpt) REVERT: R 296 GLN cc_start: 0.8928 (mm110) cc_final: 0.8512 (mp10) REVERT: R 333 GLN cc_start: 0.8408 (mt0) cc_final: 0.8032 (tp40) REVERT: R 334 TRP cc_start: 0.7543 (m100) cc_final: 0.7003 (m100) REVERT: R 354 TYR cc_start: 0.8582 (m-80) cc_final: 0.8285 (m-80) REVERT: A 206 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8298 (mmm-85) REVERT: A 208 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 243 ARG cc_start: 0.8849 (tpp80) cc_final: 0.8640 (mtm-85) REVERT: A 307 GLN cc_start: 0.9557 (mm-40) cc_final: 0.9129 (mp10) REVERT: A 333 GLN cc_start: 0.8706 (tp40) cc_final: 0.8292 (tp40) REVERT: B 10 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8698 (mm-30) REVERT: B 130 GLU cc_start: 0.9122 (mp0) cc_final: 0.8872 (mp0) REVERT: B 217 MET cc_start: 0.8196 (mtm) cc_final: 0.7847 (ptt) REVERT: B 249 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 254 ASP cc_start: 0.8467 (t70) cc_final: 0.8096 (t0) REVERT: B 325 MET cc_start: 0.9291 (tpt) cc_final: 0.9029 (tpp) REVERT: C 13 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8249 (mtm-85) REVERT: C 17 GLU cc_start: 0.9370 (tp30) cc_final: 0.9054 (mm-30) REVERT: C 20 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7671 (mtmm) REVERT: C 24 ASN cc_start: 0.8951 (m110) cc_final: 0.8672 (m110) REVERT: D 46 GLU cc_start: 0.8733 (tt0) cc_final: 0.8266 (tt0) REVERT: D 132 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8347 (p) REVERT: D 206 ARG cc_start: 0.9088 (mtm-85) cc_final: 0.8753 (mtp180) REVERT: D 208 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 210 GLU cc_start: 0.8386 (pm20) cc_final: 0.7850 (pp20) REVERT: D 211 ASP cc_start: 0.8495 (m-30) cc_final: 0.8013 (m-30) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.7472 time to fit residues: 104.5332 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 347 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.050866 restraints weight = 23303.666| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.18 r_work: 0.2551 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8969 Z= 0.134 Angle : 0.598 10.091 12159 Z= 0.309 Chirality : 0.042 0.328 1389 Planarity : 0.004 0.059 1533 Dihedral : 4.231 54.503 1222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.11 % Allowed : 16.75 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.26), residues: 1108 helix: 2.51 (0.26), residues: 404 sheet: 0.26 (0.30), residues: 292 loop : -0.61 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 8 TYR 0.016 0.001 TYR R 125 PHE 0.011 0.001 PHE R 312 TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8967) covalent geometry : angle 0.59748 / 0.31 (12155) SS BOND : bond 0.00536 / 0.27 ( 2) SS BOND : angle 0.89730 / 0.41 ( 4) hydrogen bonds : bond 0.03927 / 2.65 ( 474) hydrogen bonds : angle 4.59097 / 3.41 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8816 (mttt) cc_final: 0.8444 (mtmm) REVERT: R 112 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8605 (t0) REVERT: R 123 GLU cc_start: 0.8982 (tt0) cc_final: 0.8626 (mt-10) REVERT: R 129 TRP cc_start: 0.8415 (m100) cc_final: 0.8040 (m100) REVERT: R 187 LYS cc_start: 0.8786 (mttt) cc_final: 0.8193 (tmtt) REVERT: R 207 MET cc_start: 0.8793 (mmm) cc_final: 0.8578 (tpt) REVERT: R 296 GLN cc_start: 0.8888 (mm110) cc_final: 0.8540 (mp10) REVERT: R 300 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5883 (t-90) REVERT: R 333 GLN cc_start: 0.8502 (mt0) cc_final: 0.8135 (tp40) REVERT: R 334 TRP cc_start: 0.7507 (m100) cc_final: 0.6993 (m100) REVERT: R 354 TYR cc_start: 0.8563 (m-80) cc_final: 0.8187 (m-80) REVERT: A 206 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8383 (mmm-85) REVERT: A 243 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8531 (mtm-85) REVERT: A 307 GLN cc_start: 0.9590 (mm-40) cc_final: 0.9171 (mp10) REVERT: A 333 GLN cc_start: 0.8680 (tp40) cc_final: 0.8081 (tm-30) REVERT: B 10 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8642 (mm-30) REVERT: B 130 GLU cc_start: 0.9098 (mp0) cc_final: 0.8817 (mp0) REVERT: B 217 MET cc_start: 0.8180 (mtm) cc_final: 0.7891 (ptt) REVERT: B 254 ASP cc_start: 0.8422 (t70) cc_final: 0.8061 (t0) REVERT: B 325 MET cc_start: 0.9251 (tpt) cc_final: 0.8970 (tpp) REVERT: C 13 ARG cc_start: 0.8622 (ttp-170) cc_final: 0.8205 (mtm-85) REVERT: C 17 GLU cc_start: 0.9400 (tp30) cc_final: 0.9082 (mm-30) REVERT: C 20 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7809 (mtmm) REVERT: C 24 ASN cc_start: 0.8906 (m110) cc_final: 0.8660 (m110) REVERT: C 58 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8964 (pm20) REVERT: D 6 GLU cc_start: 0.8226 (mp0) cc_final: 0.7841 (mp0) REVERT: D 46 GLU cc_start: 0.8620 (tt0) cc_final: 0.8151 (tt0) REVERT: D 132 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8420 (p) REVERT: D 208 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 210 GLU cc_start: 0.8450 (pm20) cc_final: 0.7873 (pp20) REVERT: D 211 ASP cc_start: 0.8479 (m-30) cc_final: 0.7940 (m-30) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 0.7567 time to fit residues: 103.4919 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 300 HIS Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 ASN A 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049910 restraints weight = 23320.219| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.14 r_work: 0.2541 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8969 Z= 0.154 Angle : 0.608 11.378 12159 Z= 0.313 Chirality : 0.041 0.140 1389 Planarity : 0.004 0.063 1533 Dihedral : 4.218 54.889 1222 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 17.28 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1108 helix: 2.48 (0.26), residues: 404 sheet: 0.19 (0.30), residues: 284 loop : -0.55 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 206 TYR 0.019 0.001 TYR R 125 PHE 0.010 0.001 PHE R 312 TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8967) covalent geometry : angle 0.60814 / 0.31 (12155) SS BOND : bond 0.00571 / 0.29 ( 2) SS BOND : angle 0.94128 / 0.42 ( 4) hydrogen bonds : bond 0.04022 / 2.71 ( 474) hydrogen bonds : angle 4.60354 / 3.42 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.22 seconds wall clock time: 52 minutes 11.38 seconds (3131.38 seconds total)