Starting phenix.real_space_refine on Fri Oct 10 20:06:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbh_38218/10_2025/8xbh_38218.map" } resolution = 2.83 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 ------------------------------------------------------------------------------- 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= -0.004 sd= 0.523 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 5709 2.51 5 N 1514 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8947 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 8947 At special positions: 0 Unit cell: (90.37, 120.063, 135.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 1656 8.00 N 1514 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.74 Conformation dependent library (CDL) restraints added in 321.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.698A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.865A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.167A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.524A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.689A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.568A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.765A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.047A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 81 Processing helix chain 'R' and resid 87 through 117 Proline residue: R 108 - end of helix removed outlier: 4.161A pdb=" N GLN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.635A pdb=" N CYS R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 197 removed outlier: 3.675A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 4.038A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 294 removed outlier: 4.117A pdb=" N TYR R 261 " --> pdb=" O ASN R 257 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.046A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.994A pdb=" N LYS R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.548A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.949A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.807A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 191 removed outlier: 7.353A pdb=" N GLY A 183 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLY A 203 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.526A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.463A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.075A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.860A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.538A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.280A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.272A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.272A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN S 219 " --> pdb=" O THR S 226 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1326 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: 1.33 Time building geometry restraints manager: 0.95 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: 1572 1.33 - 1.45: 2425 1.45 - 1.57: 5032 1.57 - 1.69: 2 1.69 - 1.82: 98 Bond restraints: 9129 Sorted by residual: bond pdb=" C4 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sigma weight residual 1.414 1.469 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " ideal model delta sigma weight residual 1.519 1.469 0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" O6 KW3 R 401 " pdb=" P1 KW3 R 401 " ideal model delta sigma weight residual 1.652 1.605 0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.94e+00 ... (remaining 9124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12267 2.98 - 5.95: 71 5.95 - 8.93: 6 8.93 - 11.90: 0 11.90 - 14.88: 2 Bond angle restraints: 12346 Sorted by residual: angle pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 114.40 129.28 -14.88 2.30e+00 1.89e-01 4.19e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 110.80 117.25 -6.45 1.41e+00 5.03e-01 2.09e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.00 4.20 9.60e-01 1.09e+00 1.92e+01 angle pdb=" N CYS B 103 " pdb=" CA CYS B 103 " pdb=" C CYS B 103 " ideal model delta sigma weight residual 107.73 113.98 -6.25 1.61e+00 3.86e-01 1.51e+01 angle pdb=" CA CYS B 114 " pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 114.40 122.61 -8.21 2.30e+00 1.89e-01 1.28e+01 ... (remaining 12341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 5165 24.77 - 49.54: 245 49.54 - 74.32: 18 74.32 - 99.09: 11 99.09 - 123.86: 3 Dihedral angle restraints: 5442 sinusoidal: 2143 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 145.80 -52.80 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA CYS B 103 " pdb=" C CYS B 103 " pdb=" N ALA B 104 " pdb=" CA ALA B 104 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1095 0.050 - 0.099: 251 0.099 - 0.149: 51 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL R 280 " pdb=" CA VAL R 280 " pdb=" CG1 VAL R 280 " pdb=" CG2 VAL R 280 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1399 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 318 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE R 318 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 318 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 318 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 318 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 318 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 318 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASP B 247 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 247 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 248 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO G 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 236 2.70 - 3.25: 8761 3.25 - 3.80: 14331 3.80 - 4.35: 18834 4.35 - 4.90: 31715 Nonbonded interactions: 73877 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.151 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.199 3.120 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.218 3.040 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.238 3.040 ... (remaining 73872 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.660 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 : 0.003 0.057 9134 Z= 0.161 Angle : 0.684 14.881 12356 Z= 0.380 Chirality : 0.044 0.248 1402 Planarity : 0.004 0.041 1548 Dihedral : 14.311 123.859 3301 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1121 helix: 1.85 (0.26), residues: 396 sheet: -0.26 (0.30), residues: 297 loop : -0.98 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.020 0.002 TYR A 320 PHE 0.030 0.002 PHE R 318 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9129) covalent geometry : angle 0.67632 (12346) SS BOND : bond 0.00977 ( 5) SS BOND : angle 3.56743 ( 10) hydrogen bonds : bond 0.12014 ( 466) hydrogen bonds : angle 5.43975 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6637 (mtp-110) REVERT: A 209 LYS cc_start: 0.7908 (tttt) cc_final: 0.7678 (tttm) REVERT: A 345 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7756 (tmtp) REVERT: B 155 ASN cc_start: 0.7936 (t0) cc_final: 0.7604 (t0) REVERT: B 220 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7125 (mp10) REVERT: B 280 LYS cc_start: 0.7968 (tttm) cc_final: 0.7742 (tttp) REVERT: B 301 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7860 (mttm) REVERT: B 325 MET cc_start: 0.7818 (mmm) cc_final: 0.7597 (mmm) REVERT: S 189 ASP cc_start: 0.7363 (p0) cc_final: 0.6965 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.4689 time to fit residues: 113.0620 Evaluate side-chains 190 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 293 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.210596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.171476 restraints weight = 10451.599| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.07 r_work: 0.3696 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 9134 Z= 0.253 Angle : 0.738 11.426 12356 Z= 0.391 Chirality : 0.048 0.275 1402 Planarity : 0.005 0.053 1548 Dihedral : 10.079 134.095 1268 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.57 % Allowed : 13.36 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.25), residues: 1121 helix: 1.53 (0.26), residues: 389 sheet: -0.25 (0.30), residues: 296 loop : -1.14 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 86 TYR 0.025 0.003 TYR B 105 PHE 0.035 0.003 PHE B 151 TRP 0.015 0.002 TRP B 99 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 9129) covalent geometry : angle 0.73569 (12346) SS BOND : bond 0.00980 ( 5) SS BOND : angle 2.29972 ( 10) hydrogen bonds : bond 0.05186 ( 466) hydrogen bonds : angle 4.99143 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7491 (pt0) cc_final: 0.7259 (pm20) REVERT: A 248 LYS cc_start: 0.7910 (pttt) cc_final: 0.7510 (ptmm) REVERT: B 175 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8150 (mm110) REVERT: B 280 LYS cc_start: 0.8533 (tttm) cc_final: 0.8191 (tttp) REVERT: R 76 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7354 (mp) REVERT: R 112 MET cc_start: 0.8608 (ttp) cc_final: 0.8399 (ttp) REVERT: R 136 MET cc_start: 0.6833 (ppp) cc_final: 0.6431 (ppp) REVERT: R 169 LYS cc_start: 0.6069 (tttm) cc_final: 0.5586 (ttpt) REVERT: R 172 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6746 (mm) REVERT: S 148 ARG cc_start: 0.6432 (ptp-110) cc_final: 0.5857 (ptp90) REVERT: S 189 ASP cc_start: 0.7765 (p0) cc_final: 0.7117 (t0) outliers start: 25 outliers final: 11 residues processed: 197 average time/residue: 0.4645 time to fit residues: 98.3913 Evaluate side-chains 184 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN B 88 ASN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.211739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.173235 restraints weight = 10277.567| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.10 r_work: 0.3706 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9134 Z= 0.201 Angle : 0.670 10.877 12356 Z= 0.353 Chirality : 0.045 0.226 1402 Planarity : 0.004 0.054 1548 Dihedral : 9.901 134.534 1268 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.39 % Allowed : 16.44 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1121 helix: 1.56 (0.26), residues: 389 sheet: -0.18 (0.30), residues: 291 loop : -1.19 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 179 TYR 0.024 0.002 TYR B 264 PHE 0.030 0.002 PHE S 29 TRP 0.015 0.002 TRP B 99 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9129) covalent geometry : angle 0.66731 (12346) SS BOND : bond 0.01090 ( 5) SS BOND : angle 2.22912 ( 10) hydrogen bonds : bond 0.04650 ( 466) hydrogen bonds : angle 4.80282 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.353 Fit side-chains REVERT: A 33 GLU cc_start: 0.7496 (pt0) cc_final: 0.7293 (pm20) REVERT: A 207 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 245 GLU cc_start: 0.7860 (tp30) cc_final: 0.7544 (tp30) REVERT: A 248 LYS cc_start: 0.7877 (pttt) cc_final: 0.7417 (ptmm) REVERT: B 220 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: B 269 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7823 (mp) REVERT: R 76 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7340 (mp) REVERT: R 112 MET cc_start: 0.8587 (ttp) cc_final: 0.8372 (ttp) REVERT: R 136 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6520 (ppp) REVERT: R 157 ASN cc_start: 0.7467 (t0) cc_final: 0.7235 (t160) REVERT: R 169 LYS cc_start: 0.5883 (tttm) cc_final: 0.5524 (ttpt) REVERT: R 172 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6380 (OUTLIER) REVERT: R 192 LEU cc_start: 0.6628 (tp) cc_final: 0.6426 (tt) REVERT: R 244 ASN cc_start: 0.8086 (t0) cc_final: 0.7817 (t0) REVERT: R 302 LYS cc_start: 0.7544 (tmmt) cc_final: 0.6403 (mtpt) REVERT: S 189 ASP cc_start: 0.7727 (p0) cc_final: 0.7093 (t0) outliers start: 33 outliers final: 14 residues processed: 197 average time/residue: 0.4880 time to fit residues: 102.7721 Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 29 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.212358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.173456 restraints weight = 10560.738| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.98 r_work: 0.3711 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9134 Z= 0.177 Angle : 0.656 11.399 12356 Z= 0.343 Chirality : 0.045 0.269 1402 Planarity : 0.004 0.052 1548 Dihedral : 9.645 128.521 1268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 3.49 % Allowed : 18.71 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1121 helix: 1.64 (0.26), residues: 389 sheet: -0.06 (0.30), residues: 286 loop : -1.15 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 286 TYR 0.023 0.002 TYR B 264 PHE 0.026 0.002 PHE B 151 TRP 0.015 0.002 TRP B 99 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9129) covalent geometry : angle 0.65137 (12346) SS BOND : bond 0.00918 ( 5) SS BOND : angle 2.70022 ( 10) hydrogen bonds : bond 0.04405 ( 466) hydrogen bonds : angle 4.76493 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 248 LYS cc_start: 0.7892 (pttt) cc_final: 0.7687 (pttm) REVERT: B 220 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: R 76 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7322 (mp) REVERT: R 136 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6735 (ppp) REVERT: R 157 ASN cc_start: 0.7410 (t0) cc_final: 0.7194 (t160) REVERT: R 169 LYS cc_start: 0.5863 (tttm) cc_final: 0.5513 (ttpt) REVERT: R 172 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6381 (OUTLIER) REVERT: R 183 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6729 (tm) REVERT: R 244 ASN cc_start: 0.8088 (t0) cc_final: 0.7827 (t0) REVERT: S 189 ASP cc_start: 0.7757 (p0) cc_final: 0.7132 (t0) outliers start: 34 outliers final: 18 residues processed: 199 average time/residue: 0.4812 time to fit residues: 102.9258 Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN R 137 ASN R 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.212775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.175175 restraints weight = 10499.691| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.00 r_work: 0.3737 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9134 Z= 0.162 Angle : 0.680 18.552 12356 Z= 0.351 Chirality : 0.045 0.318 1402 Planarity : 0.004 0.050 1548 Dihedral : 9.480 122.539 1268 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 3.29 % Allowed : 21.07 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1121 helix: 1.70 (0.26), residues: 389 sheet: 0.04 (0.31), residues: 279 loop : -1.14 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 179 TYR 0.022 0.002 TYR B 264 PHE 0.021 0.002 PHE B 151 TRP 0.012 0.002 TRP B 99 HIS 0.006 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9129) covalent geometry : angle 0.66610 (12346) SS BOND : bond 0.01165 ( 5) SS BOND : angle 4.78721 ( 10) hydrogen bonds : bond 0.04255 ( 466) hydrogen bonds : angle 4.78281 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 248 LYS cc_start: 0.7843 (pttt) cc_final: 0.7365 (ptmm) REVERT: B 42 ARG cc_start: 0.6880 (mtm180) cc_final: 0.6537 (mmm160) REVERT: B 220 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: R 48 MET cc_start: 0.4025 (ttp) cc_final: 0.3418 (mpp) REVERT: R 76 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7322 (mp) REVERT: R 136 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6439 (ppp) REVERT: R 169 LYS cc_start: 0.5849 (tttm) cc_final: 0.5467 (ttpt) REVERT: R 172 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6371 (OUTLIER) REVERT: R 183 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6744 (tm) REVERT: R 244 ASN cc_start: 0.8093 (t0) cc_final: 0.7798 (t0) REVERT: R 302 LYS cc_start: 0.7561 (tmmt) cc_final: 0.6401 (mtpp) REVERT: S 189 ASP cc_start: 0.7715 (p0) cc_final: 0.7077 (t0) outliers start: 32 outliers final: 19 residues processed: 202 average time/residue: 0.4949 time to fit residues: 106.9347 Evaluate side-chains 199 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN B 183 HIS R 157 ASN R 293 GLN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.208507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170100 restraints weight = 10484.603| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.96 r_work: 0.3677 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9134 Z= 0.241 Angle : 0.760 18.013 12356 Z= 0.395 Chirality : 0.048 0.398 1402 Planarity : 0.004 0.056 1548 Dihedral : 9.651 117.782 1268 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 4.62 % Allowed : 21.07 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.01 (0.25), residues: 1121 helix: 1.45 (0.26), residues: 390 sheet: -0.07 (0.31), residues: 280 loop : -1.20 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 152 TYR 0.032 0.002 TYR B 264 PHE 0.030 0.003 PHE B 151 TRP 0.016 0.002 TRP B 99 HIS 0.007 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 9129) covalent geometry : angle 0.74696 (12346) SS BOND : bond 0.01413 ( 5) SS BOND : angle 5.05563 ( 10) hydrogen bonds : bond 0.04948 ( 466) hydrogen bonds : angle 5.00451 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: A 248 LYS cc_start: 0.7884 (pttt) cc_final: 0.7448 (ptmm) REVERT: B 220 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: R 76 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7314 (mp) REVERT: R 136 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6637 (ppp) REVERT: R 169 LYS cc_start: 0.6041 (tttm) cc_final: 0.5552 (ttpt) REVERT: R 172 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6442 (OUTLIER) REVERT: R 192 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6470 (tp) REVERT: R 244 ASN cc_start: 0.8125 (t0) cc_final: 0.7861 (t0) REVERT: R 302 LYS cc_start: 0.7764 (tmmt) cc_final: 0.6580 (mtpp) REVERT: S 189 ASP cc_start: 0.7682 (p0) cc_final: 0.7039 (t0) outliers start: 45 outliers final: 31 residues processed: 206 average time/residue: 0.4868 time to fit residues: 107.5570 Evaluate side-chains 209 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain R residue 323 ASP Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN A 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.213325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176566 restraints weight = 10565.682| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.08 r_work: 0.3741 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9134 Z= 0.132 Angle : 0.653 15.676 12356 Z= 0.337 Chirality : 0.044 0.303 1402 Planarity : 0.004 0.050 1548 Dihedral : 9.192 114.166 1268 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 3.29 % Allowed : 23.12 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1121 helix: 1.74 (0.26), residues: 389 sheet: 0.10 (0.31), residues: 272 loop : -1.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 179 TYR 0.022 0.001 TYR S 178 PHE 0.018 0.002 PHE B 151 TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9129) covalent geometry : angle 0.64143 (12346) SS BOND : bond 0.00673 ( 5) SS BOND : angle 4.42022 ( 10) hydrogen bonds : bond 0.03937 ( 466) hydrogen bonds : angle 4.68269 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.376 Fit side-chains REVERT: A 207 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 248 LYS cc_start: 0.7778 (pttt) cc_final: 0.7407 (ptmm) REVERT: B 42 ARG cc_start: 0.7128 (mtm180) cc_final: 0.6299 (mmm160) REVERT: B 220 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: R 76 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7186 (mp) REVERT: R 136 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6745 (ppp) REVERT: R 169 LYS cc_start: 0.5861 (tttm) cc_final: 0.5479 (ttpt) REVERT: R 172 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6454 (OUTLIER) REVERT: R 183 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6677 (tm) REVERT: R 189 MET cc_start: 0.5296 (mmp) cc_final: 0.4574 (mmm) REVERT: R 191 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6427 (mp) REVERT: R 244 ASN cc_start: 0.8079 (t0) cc_final: 0.7787 (t0) REVERT: S 157 ASN cc_start: 0.7409 (m-40) cc_final: 0.7191 (m110) REVERT: S 189 ASP cc_start: 0.7657 (p0) cc_final: 0.7026 (t0) REVERT: S 200 PHE cc_start: 0.7154 (m-80) cc_final: 0.6919 (m-80) outliers start: 32 outliers final: 15 residues processed: 203 average time/residue: 0.5326 time to fit residues: 116.1576 Evaluate side-chains 197 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.212774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174991 restraints weight = 10344.677| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.02 r_work: 0.3731 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9134 Z= 0.164 Angle : 0.714 22.993 12356 Z= 0.365 Chirality : 0.045 0.274 1402 Planarity : 0.004 0.050 1548 Dihedral : 9.216 113.126 1268 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 3.60 % Allowed : 23.23 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.22 (0.25), residues: 1121 helix: 1.67 (0.26), residues: 392 sheet: -0.01 (0.30), residues: 280 loop : -1.10 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 67 TYR 0.021 0.002 TYR S 178 PHE 0.023 0.002 PHE B 151 TRP 0.013 0.001 TRP B 99 HIS 0.008 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9129) covalent geometry : angle 0.69967 (12346) SS BOND : bond 0.01007 ( 5) SS BOND : angle 5.11232 ( 10) hydrogen bonds : bond 0.04231 ( 466) hydrogen bonds : angle 4.72955 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.330 Fit side-chains REVERT: A 207 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 248 LYS cc_start: 0.7776 (pttt) cc_final: 0.7343 (ptmm) REVERT: B 220 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: B 262 MET cc_start: 0.7501 (tpt) cc_final: 0.7286 (tpp) REVERT: R 48 MET cc_start: 0.2573 (ptm) cc_final: 0.1906 (mpp) REVERT: R 76 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7276 (mp) REVERT: R 136 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6554 (ppp) REVERT: R 169 LYS cc_start: 0.6013 (tttm) cc_final: 0.5652 (ttpt) REVERT: R 172 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6405 (OUTLIER) REVERT: R 191 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6327 (mp) REVERT: R 244 ASN cc_start: 0.8003 (t0) cc_final: 0.7695 (t0) REVERT: R 302 LYS cc_start: 0.7779 (tmmt) cc_final: 0.6475 (mtpp) REVERT: S 76 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7466 (mppt) REVERT: S 189 ASP cc_start: 0.7734 (p0) cc_final: 0.7088 (t0) outliers start: 35 outliers final: 21 residues processed: 199 average time/residue: 0.5017 time to fit residues: 107.1622 Evaluate side-chains 200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 323 ASP Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.212291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.174566 restraints weight = 10320.348| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.03 r_work: 0.3721 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9134 Z= 0.171 Angle : 0.744 25.126 12356 Z= 0.378 Chirality : 0.046 0.292 1402 Planarity : 0.004 0.051 1548 Dihedral : 9.215 112.583 1268 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 3.80 % Allowed : 23.84 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.18 (0.25), residues: 1121 helix: 1.63 (0.26), residues: 392 sheet: -0.03 (0.30), residues: 280 loop : -1.12 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 86 TYR 0.021 0.002 TYR S 178 PHE 0.033 0.002 PHE S 29 TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9129) covalent geometry : angle 0.72563 (12346) SS BOND : bond 0.01253 ( 5) SS BOND : angle 5.74599 ( 10) hydrogen bonds : bond 0.04298 ( 466) hydrogen bonds : angle 4.74133 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 248 LYS cc_start: 0.7808 (pttt) cc_final: 0.7570 (pttm) REVERT: R 48 MET cc_start: 0.3010 (ptm) cc_final: 0.2225 (mpp) REVERT: R 76 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7286 (mp) REVERT: R 136 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6554 (ppp) REVERT: R 169 LYS cc_start: 0.5930 (tttm) cc_final: 0.5548 (ttpt) REVERT: R 172 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6499 (OUTLIER) REVERT: R 183 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6626 (tm) REVERT: R 191 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6325 (mp) REVERT: R 244 ASN cc_start: 0.8113 (t0) cc_final: 0.7812 (t0) REVERT: R 302 LYS cc_start: 0.7773 (tmmt) cc_final: 0.6478 (mtpp) REVERT: S 76 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7306 (mppt) REVERT: S 189 ASP cc_start: 0.7734 (p0) cc_final: 0.7078 (t0) outliers start: 37 outliers final: 26 residues processed: 198 average time/residue: 0.5468 time to fit residues: 116.0885 Evaluate side-chains 202 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 323 ASP Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.212263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.174416 restraints weight = 10331.847| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.99 r_work: 0.3717 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.004 0.072 9134 Z= 0.173 Angle : 0.741 21.859 12356 Z= 0.376 Chirality : 0.046 0.327 1402 Planarity : 0.004 0.051 1548 Dihedral : 9.214 114.303 1268 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 3.70 % Allowed : 24.05 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.15 (0.25), residues: 1121 helix: 1.61 (0.26), residues: 392 sheet: -0.03 (0.30), residues: 280 loop : -1.15 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 86 TYR 0.021 0.002 TYR S 178 PHE 0.032 0.002 PHE S 29 TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9129) covalent geometry : angle 0.72474 (12346) SS BOND : bond 0.01201 ( 5) SS BOND : angle 5.41815 ( 10) hydrogen bonds : bond 0.04335 ( 466) hydrogen bonds : angle 4.76636 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 248 LYS cc_start: 0.7837 (pttt) cc_final: 0.7628 (pttm) REVERT: B 262 MET cc_start: 0.7543 (tpt) cc_final: 0.7308 (tpp) REVERT: R 76 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7288 (mp) REVERT: R 136 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6752 (ppp) REVERT: R 169 LYS cc_start: 0.5992 (tttm) cc_final: 0.5605 (ttpt) REVERT: R 172 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6541 (OUTLIER) REVERT: R 183 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6629 (tm) REVERT: R 191 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6325 (mp) REVERT: R 244 ASN cc_start: 0.8118 (t0) cc_final: 0.7827 (t0) REVERT: R 302 LYS cc_start: 0.7789 (tmmt) cc_final: 0.6417 (mtpp) REVERT: S 76 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7321 (mppt) REVERT: S 189 ASP cc_start: 0.7787 (p0) cc_final: 0.7110 (t0) outliers start: 36 outliers final: 26 residues processed: 197 average time/residue: 0.5234 time to fit residues: 110.8804 Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 323 ASP Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 0.0670 chunk 71 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.212026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174252 restraints weight = 10222.262| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.04 r_work: 0.3719 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9134 Z= 0.180 Angle : 0.759 25.644 12356 Z= 0.385 Chirality : 0.046 0.286 1402 Planarity : 0.004 0.052 1548 Dihedral : 9.256 116.755 1268 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 3.70 % Allowed : 24.36 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.13 (0.25), residues: 1121 helix: 1.62 (0.26), residues: 391 sheet: -0.06 (0.30), residues: 280 loop : -1.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 86 TYR 0.021 0.002 TYR S 178 PHE 0.032 0.002 PHE S 29 TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9129) covalent geometry : angle 0.74181 (12346) SS BOND : bond 0.01324 ( 5) SS BOND : angle 5.73855 ( 10) hydrogen bonds : bond 0.04424 ( 466) hydrogen bonds : angle 4.78174 ( 1326) =============================================================================== Job complete usr+sys time: 3906.50 seconds wall clock time: 67 minutes 19.80 seconds (4039.80 seconds total)