Starting phenix.real_space_refine on Fri Aug 22 23:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914.map" model { file = "/net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j19_35914/08_2025/8j19_35914_neut.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 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 59 5.16 5 C 5619 2.51 5 N 1509 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2232 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'SWO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.18 Number of scatterers: 8801 At special positions: 0 Unit cell: (96.408, 117.832, 124.424, 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 59 16.00 O 1614 8.00 N 1509 7.00 C 5619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.12 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=1.66 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 206.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 39.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 14 through 18 removed outlier: 4.094A pdb=" N GLY R 18 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 48 Processing helix chain 'R' and resid 49 through 52 removed outlier: 3.579A pdb=" N ARG R 52 " --> pdb=" O PRO R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 55 through 84 removed outlier: 4.054A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN R 74 " --> pdb=" O CYS R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 89 through 124 removed outlier: 3.873A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU R 98 " --> pdb=" O ARG R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 151 removed outlier: 4.658A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 157 Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 175 through 212 removed outlier: 3.851A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 316 through 342 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 348 through 371 removed outlier: 4.306A pdb=" N HIS R 352 " --> pdb=" O PRO R 348 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET R 353 " --> pdb=" O ARG R 349 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS R 364 " --> pdb=" O TRP R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 removed outlier: 3.696A pdb=" N GLN R 379 " --> pdb=" O ARG R 375 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA R 380 " --> pdb=" O GLN R 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.734A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 4.203A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.331A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.920A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.013A 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 62 through 65 removed outlier: 3.625A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.569A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'R' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.665A pdb=" N PHE A 196 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.084A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.668A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.976A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.459A 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: 3.536A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.140A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.922A 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: 4.319A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.866A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.537A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1239 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: 1.17 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1409 1.32 - 1.44: 2494 1.44 - 1.57: 4997 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 8984 Sorted by residual: bond pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 1.334 1.434 -0.100 1.49e-02 4.50e+03 4.52e+01 bond pdb=" C03 SWO R 401 " pdb=" N04 SWO R 401 " ideal model delta sigma weight residual 1.348 1.240 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" CA TRP R 156 " pdb=" C TRP R 156 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C TRP R 156 " pdb=" N PRO R 157 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" C ILE R 333 " pdb=" O ILE R 333 " ideal model delta sigma weight residual 1.240 1.198 0.042 1.26e-02 6.30e+03 1.12e+01 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 12043 2.42 - 4.85: 108 4.85 - 7.27: 16 7.27 - 9.69: 4 9.69 - 12.11: 3 Bond angle restraints: 12174 Sorted by residual: angle pdb=" N GLY R 315 " pdb=" CA GLY R 315 " pdb=" C GLY R 315 " ideal model delta sigma weight residual 114.37 102.26 12.11 1.26e+00 6.30e-01 9.24e+01 angle pdb=" O ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 121.87 112.94 8.93 1.01e+00 9.80e-01 7.82e+01 angle pdb=" N ILE R 340 " pdb=" CA ILE R 340 " pdb=" C ILE R 340 " ideal model delta sigma weight residual 111.56 105.89 5.67 8.60e-01 1.35e+00 4.35e+01 angle pdb=" CA ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 117.53 123.82 -6.29 1.19e+00 7.06e-01 2.79e+01 angle pdb=" N VAL S 5 " pdb=" CA VAL S 5 " pdb=" C VAL S 5 " ideal model delta sigma weight residual 109.17 101.82 7.35 1.54e+00 4.22e-01 2.28e+01 ... (remaining 12169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4676 17.72 - 35.44: 482 35.44 - 53.16: 119 53.16 - 70.88: 27 70.88 - 88.60: 13 Dihedral angle restraints: 5317 sinusoidal: 2048 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS R 93 " pdb=" SG CYS R 93 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C ILE R 333 " pdb=" N ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual 123.40 132.76 -9.36 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1207 0.058 - 0.117: 156 0.117 - 0.175: 22 0.175 - 0.233: 4 0.233 - 0.291: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA VAL S 5 " pdb=" N VAL S 5 " pdb=" C VAL S 5 " pdb=" CB VAL S 5 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE R 333 " pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CB ILE R 333 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE R 340 " pdb=" N ILE R 340 " pdb=" C ILE R 340 " pdb=" CB ILE R 340 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1388 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 185 " -0.030 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ILE R 185 " 0.092 2.00e-02 2.50e+03 pdb=" O ILE R 185 " -0.033 2.00e-02 2.50e+03 pdb=" N TYR R 186 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 SWO R 401 " -0.003 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" C02 SWO R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C03 SWO R 401 " -0.033 2.00e-02 2.50e+03 pdb=" C05 SWO R 401 " 0.007 2.00e-02 2.50e+03 pdb=" C06 SWO R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C07 SWO R 401 " -0.012 2.00e-02 2.50e+03 pdb=" N04 SWO R 401 " 0.050 2.00e-02 2.50e+03 pdb=" O16 SWO R 401 " -0.003 2.00e-02 2.50e+03 pdb=" O17 SWO R 401 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLY R 175 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.018 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1360 2.76 - 3.29: 8581 3.29 - 3.83: 14329 3.83 - 4.36: 17107 4.36 - 4.90: 30885 Nonbonded interactions: 72262 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.274 3.040 nonbonded pdb=" O ALA R 31 " pdb=" OG1 THR R 35 " model vdw 2.275 3.040 nonbonded pdb=" ND1 HIS S 167 " pdb=" OD1 ASN S 169 " model vdw 2.289 3.120 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.290 3.040 ... (remaining 72257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.371 8987 Z= 0.312 Angle : 0.787 45.307 12180 Z= 0.437 Chirality : 0.043 0.291 1391 Planarity : 0.005 0.078 1533 Dihedral : 15.950 88.596 3202 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.74 % Allowed : 17.11 % Favored : 82.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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: 0.90 (0.26), residues: 1111 helix: 2.32 (0.28), residues: 368 sheet: -0.11 (0.32), residues: 292 loop : -0.30 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 54 TYR 0.009 0.001 TYR S 190 PHE 0.009 0.001 PHE S 80 TRP 0.024 0.001 TRP R 156 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8984) covalent geometry : angle 0.64043 (12174) SS BOND : bond 0.22001 ( 3) SS BOND : angle 20.61707 ( 6) hydrogen bonds : bond 0.17794 ( 445) hydrogen bonds : angle 7.10602 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.211 Fit side-chains REVERT: R 88 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (p) REVERT: R 313 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: R 316 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7876 (tptt) REVERT: R 349 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5572 (mtp180) REVERT: A 255 ASN cc_start: 0.8380 (m-40) cc_final: 0.8161 (m110) REVERT: B 323 ASP cc_start: 0.8538 (p0) cc_final: 0.8317 (p0) REVERT: S 179 GLN cc_start: 0.8824 (tt0) cc_final: 0.8621 (tt0) outliers start: 7 outliers final: 0 residues processed: 119 average time/residue: 0.0842 time to fit residues: 13.5223 Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 313 GLU Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 349 ARG 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: 3.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 352 HIS A 269 ASN B 75 GLN B 142 HIS B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.174511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135284 restraints weight = 9994.167| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.07 r_work: 0.3389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8987 Z= 0.281 Angle : 0.675 9.656 12180 Z= 0.354 Chirality : 0.047 0.162 1391 Planarity : 0.005 0.049 1533 Dihedral : 5.972 52.396 1245 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.54 % Allowed : 15.31 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.25), residues: 1111 helix: 1.80 (0.27), residues: 373 sheet: -0.45 (0.30), residues: 292 loop : -0.47 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 172 TYR 0.026 0.002 TYR B 59 PHE 0.024 0.002 PHE B 235 TRP 0.019 0.002 TRP S 47 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 8984) covalent geometry : angle 0.67485 (12174) SS BOND : bond 0.01179 ( 3) SS BOND : angle 1.09586 ( 6) hydrogen bonds : bond 0.04612 ( 445) hydrogen bonds : angle 5.36956 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.226 Fit side-chains REVERT: R 316 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7449 (tptt) REVERT: A 49 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6398 (tp) REVERT: A 255 ASN cc_start: 0.8493 (m-40) cc_final: 0.8219 (m110) REVERT: B 57 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8660 (mttp) REVERT: B 170 ASP cc_start: 0.8332 (t0) cc_final: 0.8121 (t0) REVERT: S 113 GLN cc_start: 0.8717 (tp40) cc_final: 0.8451 (mm-40) REVERT: S 159 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8232 (t) REVERT: S 179 GLN cc_start: 0.8791 (tt0) cc_final: 0.8324 (tt0) REVERT: S 193 SER cc_start: 0.8369 (t) cc_final: 0.8150 (t) REVERT: S 204 SER cc_start: 0.9034 (t) cc_final: 0.8588 (p) outliers start: 43 outliers final: 21 residues processed: 141 average time/residue: 0.0748 time to fit residues: 14.5927 Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 ASN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140303 restraints weight = 9800.238| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.04 r_work: 0.3466 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8987 Z= 0.114 Angle : 0.519 6.662 12180 Z= 0.271 Chirality : 0.041 0.139 1391 Planarity : 0.004 0.042 1533 Dihedral : 5.120 59.357 1238 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.75 % Allowed : 18.06 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.26), residues: 1111 helix: 2.10 (0.27), residues: 369 sheet: -0.31 (0.31), residues: 274 loop : -0.35 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.011 0.001 TYR R 186 PHE 0.012 0.001 PHE S 27 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8984) covalent geometry : angle 0.51786 (12174) SS BOND : bond 0.00250 ( 3) SS BOND : angle 1.51898 ( 6) hydrogen bonds : bond 0.03488 ( 445) hydrogen bonds : angle 4.89920 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.299 Fit side-chains REVERT: R 316 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7358 (ttmt) REVERT: R 326 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 8 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: A 255 ASN cc_start: 0.8293 (m-40) cc_final: 0.8079 (m110) REVERT: A 306 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6737 (mm110) REVERT: S 83 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8095 (ptm) REVERT: S 204 SER cc_start: 0.9017 (t) cc_final: 0.8533 (p) outliers start: 26 outliers final: 14 residues processed: 139 average time/residue: 0.0657 time to fit residues: 13.0576 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN B 125 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132801 restraints weight = 10025.962| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.10 r_work: 0.3365 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8987 Z= 0.236 Angle : 0.609 7.705 12180 Z= 0.319 Chirality : 0.044 0.146 1391 Planarity : 0.004 0.043 1533 Dihedral : 5.277 59.866 1237 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.44 % Allowed : 18.06 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.33 (0.25), residues: 1111 helix: 1.82 (0.27), residues: 368 sheet: -0.51 (0.30), residues: 290 loop : -0.54 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.013 0.002 TYR S 190 PHE 0.019 0.002 PHE B 235 TRP 0.015 0.002 TRP S 47 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8984) covalent geometry : angle 0.60848 (12174) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.45623 ( 6) hydrogen bonds : bond 0.04022 ( 445) hydrogen bonds : angle 4.99554 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.203 Fit side-chains REVERT: R 316 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7473 (ttmt) REVERT: R 326 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7393 (tp) REVERT: A 8 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: A 255 ASN cc_start: 0.8394 (m-40) cc_final: 0.8133 (m110) REVERT: B 57 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8532 (mttp) REVERT: B 146 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8100 (mp) REVERT: S 83 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8218 (ptm) REVERT: S 204 SER cc_start: 0.9046 (t) cc_final: 0.8564 (p) outliers start: 42 outliers final: 25 residues processed: 143 average time/residue: 0.0786 time to fit residues: 15.6189 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135086 restraints weight = 9937.610| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.20 r_work: 0.3382 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8987 Z= 0.181 Angle : 0.570 8.345 12180 Z= 0.297 Chirality : 0.042 0.139 1391 Planarity : 0.004 0.040 1533 Dihedral : 5.179 58.321 1237 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.96 % Allowed : 17.85 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.25), residues: 1111 helix: 1.80 (0.27), residues: 369 sheet: -0.59 (0.30), residues: 284 loop : -0.64 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.012 0.001 TYR S 190 PHE 0.016 0.002 PHE B 235 TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8984) covalent geometry : angle 0.56960 (12174) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.21438 ( 6) hydrogen bonds : bond 0.03732 ( 445) hydrogen bonds : angle 4.91938 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.232 Fit side-chains REVERT: R 316 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7470 (ttmt) REVERT: R 326 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7347 (tp) REVERT: A 8 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: A 255 ASN cc_start: 0.8369 (m-40) cc_final: 0.8105 (m110) REVERT: B 13 GLN cc_start: 0.7441 (mp10) cc_final: 0.7209 (pt0) REVERT: B 57 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8477 (mttp) REVERT: B 259 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: S 38 ARG cc_start: 0.8525 (ptt180) cc_final: 0.8286 (ptt90) REVERT: S 204 SER cc_start: 0.9012 (t) cc_final: 0.8532 (p) outliers start: 47 outliers final: 30 residues processed: 151 average time/residue: 0.0671 time to fit residues: 14.2624 Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138193 restraints weight = 10003.400| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.12 r_work: 0.3436 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8987 Z= 0.112 Angle : 0.517 6.623 12180 Z= 0.267 Chirality : 0.040 0.134 1391 Planarity : 0.004 0.035 1533 Dihedral : 4.947 58.599 1237 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.70 % Allowed : 20.17 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.43 (0.26), residues: 1111 helix: 2.04 (0.28), residues: 369 sheet: -0.65 (0.31), residues: 266 loop : -0.49 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.010 0.001 TYR S 190 PHE 0.011 0.001 PHE S 27 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8984) covalent geometry : angle 0.51645 (12174) SS BOND : bond 0.00531 ( 3) SS BOND : angle 1.16919 ( 6) hydrogen bonds : bond 0.03272 ( 445) hydrogen bonds : angle 4.71811 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.217 Fit side-chains REVERT: R 203 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.6791 (mtp180) REVERT: R 316 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7451 (ttmt) REVERT: R 326 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 8 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: A 248 LYS cc_start: 0.8207 (mttm) cc_final: 0.7973 (mttp) REVERT: A 255 ASN cc_start: 0.8272 (m-40) cc_final: 0.8054 (m110) REVERT: B 13 GLN cc_start: 0.7437 (mp10) cc_final: 0.7203 (pt0) REVERT: B 19 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8268 (ttp80) REVERT: B 57 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: B 259 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: S 38 ARG cc_start: 0.8499 (ptt180) cc_final: 0.8253 (ptt90) REVERT: S 58 ILE cc_start: 0.8968 (mt) cc_final: 0.8722 (mt) REVERT: S 204 SER cc_start: 0.9017 (t) cc_final: 0.8313 (p) outliers start: 35 outliers final: 26 residues processed: 147 average time/residue: 0.0752 time to fit residues: 15.1877 Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137121 restraints weight = 9938.039| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.99 r_work: 0.3438 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8987 Z= 0.140 Angle : 0.539 7.611 12180 Z= 0.277 Chirality : 0.041 0.135 1391 Planarity : 0.004 0.048 1533 Dihedral : 4.929 59.596 1237 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.33 % Allowed : 19.64 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.42 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 369 sheet: -0.65 (0.31), residues: 266 loop : -0.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 160 TYR 0.011 0.001 TYR S 190 PHE 0.012 0.001 PHE B 235 TRP 0.019 0.001 TRP R 360 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8984) covalent geometry : angle 0.53793 (12174) SS BOND : bond 0.00299 ( 3) SS BOND : angle 1.24850 ( 6) hydrogen bonds : bond 0.03349 ( 445) hydrogen bonds : angle 4.66330 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.187 Fit side-chains REVERT: R 316 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7435 (ttmt) REVERT: R 326 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7089 (mt) REVERT: A 8 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 248 LYS cc_start: 0.8213 (mttm) cc_final: 0.7980 (mttp) REVERT: A 255 ASN cc_start: 0.8256 (m-40) cc_final: 0.8038 (m110) REVERT: B 13 GLN cc_start: 0.7443 (mp10) cc_final: 0.7179 (pt0) REVERT: B 19 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8344 (ttp80) REVERT: B 57 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: B 259 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: S 38 ARG cc_start: 0.8476 (ptt180) cc_final: 0.8265 (ptm-80) REVERT: S 58 ILE cc_start: 0.8976 (mt) cc_final: 0.8723 (mt) REVERT: S 204 SER cc_start: 0.8964 (t) cc_final: 0.8306 (p) outliers start: 41 outliers final: 34 residues processed: 143 average time/residue: 0.0682 time to fit residues: 13.5884 Evaluate side-chains 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136646 restraints weight = 9835.001| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.09 r_work: 0.3408 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8987 Z= 0.135 Angle : 0.541 9.603 12180 Z= 0.276 Chirality : 0.041 0.135 1391 Planarity : 0.004 0.039 1533 Dihedral : 4.897 59.471 1237 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.65 % Allowed : 19.75 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.44 (0.26), residues: 1111 helix: 2.07 (0.28), residues: 369 sheet: -0.67 (0.31), residues: 268 loop : -0.48 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 160 TYR 0.011 0.001 TYR S 190 PHE 0.012 0.001 PHE B 235 TRP 0.014 0.001 TRP R 360 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8984) covalent geometry : angle 0.54078 (12174) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.35165 ( 6) hydrogen bonds : bond 0.03311 ( 445) hydrogen bonds : angle 4.62843 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.209 Fit side-chains REVERT: R 316 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7486 (ttmt) REVERT: R 326 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7162 (mt) REVERT: A 8 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: A 24 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: A 248 LYS cc_start: 0.8246 (mttm) cc_final: 0.8011 (mttp) REVERT: A 255 ASN cc_start: 0.8281 (m-40) cc_final: 0.8060 (m110) REVERT: B 13 GLN cc_start: 0.7449 (mp10) cc_final: 0.7162 (pt0) REVERT: B 19 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8247 (ttp80) REVERT: B 57 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8299 (mttp) REVERT: B 259 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: S 58 ILE cc_start: 0.8982 (mt) cc_final: 0.8745 (mt) REVERT: S 140 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.7691 (mmm) REVERT: S 204 SER cc_start: 0.8987 (t) cc_final: 0.8341 (p) outliers start: 44 outliers final: 34 residues processed: 147 average time/residue: 0.0740 time to fit residues: 15.1571 Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138481 restraints weight = 9938.955| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.08 r_work: 0.3435 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8987 Z= 0.128 Angle : 0.532 10.160 12180 Z= 0.272 Chirality : 0.041 0.135 1391 Planarity : 0.004 0.035 1533 Dihedral : 4.853 58.624 1237 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.33 % Allowed : 19.75 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.45 (0.26), residues: 1111 helix: 2.09 (0.28), residues: 369 sheet: -0.66 (0.30), residues: 282 loop : -0.46 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.011 0.001 TYR S 190 PHE 0.011 0.001 PHE B 235 TRP 0.013 0.001 TRP R 360 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8984) covalent geometry : angle 0.53079 (12174) SS BOND : bond 0.00300 ( 3) SS BOND : angle 1.45748 ( 6) hydrogen bonds : bond 0.03244 ( 445) hydrogen bonds : angle 4.60449 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.271 Fit side-chains REVERT: R 316 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7487 (ttmt) REVERT: R 326 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7158 (mt) REVERT: A 8 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: A 248 LYS cc_start: 0.8228 (mttm) cc_final: 0.8004 (mttp) REVERT: A 255 ASN cc_start: 0.8256 (m-40) cc_final: 0.8022 (m110) REVERT: B 13 GLN cc_start: 0.7491 (mp10) cc_final: 0.7190 (pt0) REVERT: B 19 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8271 (ttp80) REVERT: B 57 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8269 (mttp) REVERT: B 259 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: S 11 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8253 (tt) REVERT: S 58 ILE cc_start: 0.8969 (mt) cc_final: 0.8731 (mt) REVERT: S 204 SER cc_start: 0.9005 (t) cc_final: 0.8373 (p) outliers start: 41 outliers final: 33 residues processed: 141 average time/residue: 0.0705 time to fit residues: 14.0097 Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140483 restraints weight = 9833.807| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.00 r_work: 0.3480 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8987 Z= 0.104 Angle : 0.516 10.761 12180 Z= 0.263 Chirality : 0.040 0.135 1391 Planarity : 0.004 0.035 1533 Dihedral : 4.731 57.604 1237 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.48 % Allowed : 20.80 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.26), residues: 1111 helix: 2.16 (0.28), residues: 372 sheet: -0.58 (0.31), residues: 282 loop : -0.37 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.010 0.001 TYR S 190 PHE 0.010 0.001 PHE S 68 TRP 0.012 0.001 TRP R 360 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8984) covalent geometry : angle 0.51549 (12174) SS BOND : bond 0.00271 ( 3) SS BOND : angle 1.20684 ( 6) hydrogen bonds : bond 0.03058 ( 445) hydrogen bonds : angle 4.50573 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.187 Fit side-chains REVERT: R 174 ARG cc_start: 0.6630 (ptm160) cc_final: 0.6409 (ptm160) REVERT: R 316 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7446 (ttmt) REVERT: R 326 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7130 (mt) REVERT: A 8 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: A 20 ASP cc_start: 0.8739 (t70) cc_final: 0.8322 (m-30) REVERT: A 255 ASN cc_start: 0.8122 (m-40) cc_final: 0.7856 (m110) REVERT: B 13 GLN cc_start: 0.7505 (mp10) cc_final: 0.7186 (pt0) REVERT: B 19 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8266 (ttp80) REVERT: B 259 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: S 11 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8295 (tt) REVERT: S 58 ILE cc_start: 0.8894 (mt) cc_final: 0.8645 (mt) REVERT: S 204 SER cc_start: 0.8990 (t) cc_final: 0.8348 (p) outliers start: 33 outliers final: 26 residues processed: 135 average time/residue: 0.0673 time to fit residues: 12.8831 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 0.0370 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142231 restraints weight = 9840.819| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.00 r_work: 0.3487 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8987 Z= 0.097 Angle : 0.506 10.580 12180 Z= 0.258 Chirality : 0.039 0.134 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.639 56.882 1237 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.27 % Allowed : 21.33 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.68 (0.26), residues: 1111 helix: 2.21 (0.28), residues: 376 sheet: -0.45 (0.31), residues: 279 loop : -0.38 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.010 0.001 TYR S 190 PHE 0.011 0.001 PHE S 68 TRP 0.010 0.001 TRP R 360 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8984) covalent geometry : angle 0.50549 (12174) SS BOND : bond 0.00275 ( 3) SS BOND : angle 1.05180 ( 6) hydrogen bonds : bond 0.02959 ( 445) hydrogen bonds : angle 4.42046 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.82 seconds wall clock time: 34 minutes 52.62 seconds (2092.62 seconds total)