Starting phenix.real_space_refine on Sun May 3 00:28:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzg_48756/05_2026/9mzg_48756.cif" } resolution = 3.0 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= 0.004 sd= 0.097 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 56 5.16 5 C 5919 2.51 5 N 1642 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 245 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3159 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 15, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1920 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 2.58, per 1000 atoms: 0.28 Number of scatterers: 9339 At special positions: 0 Unit cell: (82.45, 99.45, 172.55, 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 56 16.00 O 1722 8.00 N 1642 7.00 C 5919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 269.5 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'P' and resid 3 through 29 Processing helix chain 'R' and resid 28 through 50 removed outlier: 3.587A pdb=" N HIS R 45 " --> pdb=" O ASP R 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN R 46 " --> pdb=" O GLN R 42 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU R 47 " --> pdb=" O CYS R 43 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER R 48 " --> pdb=" O HIS R 44 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.532A pdb=" N GLU R 129 " --> pdb=" O GLY R 125 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS R 132 " --> pdb=" O ILE R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.662A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 221 through 254 removed outlier: 3.523A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.537A pdb=" N TYR R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 289 removed outlier: 4.159A pdb=" N MET R 276 " --> pdb=" O TRP R 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 336 removed outlier: 3.518A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 359 removed outlier: 3.936A pdb=" N ALA R 348 " --> pdb=" O LYS R 344 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 4.496A pdb=" N PHE R 367 " --> pdb=" O VAL R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 402 removed outlier: 4.320A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 removed outlier: 3.572A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.831A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.568A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.605A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.678A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.649A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.509A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.550A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 214 removed outlier: 4.039A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 48 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 249 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.564A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.718A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.745A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.579A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.838A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.074A 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: 4.020A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.625A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.524A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1317 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: 1.89 Time building geometry restraints manager: 1.15 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: 1538 1.32 - 1.44: 2689 1.44 - 1.57: 5237 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 9541 Sorted by residual: bond pdb=" CA SER P 2 " pdb=" CB SER P 2 " ideal model delta sigma weight residual 1.536 1.452 0.084 1.53e-02 4.27e+03 3.03e+01 bond pdb=" C MET G 21 " pdb=" N GLU G 22 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.38e-02 5.25e+03 1.50e+01 bond pdb=" C LEU N 86 " pdb=" N LYS N 87 " ideal model delta sigma weight residual 1.327 1.266 0.061 1.71e-02 3.42e+03 1.27e+01 bond pdb=" C LYS R 132 " pdb=" N GLU R 133 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.31e-02 5.83e+03 1.22e+01 bond pdb=" N THR P 5 " pdb=" CA THR P 5 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.33e-02 5.65e+03 1.15e+01 ... (remaining 9536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12041 1.83 - 3.66: 794 3.66 - 5.48: 70 5.48 - 7.31: 12 7.31 - 9.14: 4 Bond angle restraints: 12921 Sorted by residual: angle pdb=" CA HIS P 1 " pdb=" CB HIS P 1 " pdb=" CG HIS P 1 " ideal model delta sigma weight residual 113.80 120.83 -7.03 1.00e+00 1.00e+00 4.94e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.22 118.32 3.90 6.50e-01 2.37e+00 3.60e+01 angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 111.28 117.31 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" N HIS P 1 " pdb=" CA HIS P 1 " pdb=" CB HIS P 1 " ideal model delta sigma weight residual 110.50 101.36 9.14 1.70e+00 3.46e-01 2.89e+01 angle pdb=" N LYS R 132 " pdb=" CA LYS R 132 " pdb=" C LYS R 132 " ideal model delta sigma weight residual 111.69 105.17 6.52 1.23e+00 6.61e-01 2.81e+01 ... (remaining 12916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5193 17.98 - 35.96: 388 35.96 - 53.93: 57 53.93 - 71.91: 12 71.91 - 89.89: 9 Dihedral angle restraints: 5659 sinusoidal: 2256 harmonic: 3403 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual 93.00 -177.11 -89.89 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -26.93 -59.07 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" N HIS P 1 " pdb=" C HIS P 1 " pdb=" CA HIS P 1 " pdb=" CB HIS P 1 " ideal model delta harmonic sigma weight residual 122.80 111.21 11.59 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 5656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1109 0.058 - 0.116: 219 0.116 - 0.173: 65 0.173 - 0.231: 21 0.231 - 0.289: 6 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ASN R 291 " pdb=" N ASN R 291 " pdb=" C ASN R 291 " pdb=" CB ASN R 291 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA THR B 243 " pdb=" N THR B 243 " pdb=" C THR B 243 " pdb=" CB THR B 243 " both_signs ideal model delta sigma weight residual False 2.53 2.80 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1417 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP P 25 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C TRP P 25 " -0.068 2.00e-02 2.50e+03 pdb=" O TRP P 25 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU P 26 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.38e+01 pdb=" NE ARG A 265 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER P 2 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C SER P 2 " -0.047 2.00e-02 2.50e+03 pdb=" O SER P 2 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN P 3 " 0.016 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1473 2.77 - 3.30: 8729 3.30 - 3.83: 14750 3.83 - 4.37: 18682 4.37 - 4.90: 32021 Nonbonded interactions: 75655 Sorted by model distance: nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.232 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.287 3.120 ... (remaining 75650 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.010 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 0.084 9547 Z= 0.456 Angle : 0.897 9.138 12933 Z= 0.646 Chirality : 0.058 0.289 1420 Planarity : 0.006 0.150 1654 Dihedral : 13.072 86.315 3441 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.20 % Allowed : 1.59 % Favored : 98.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1155 helix: 0.55 (0.23), residues: 452 sheet: 0.27 (0.33), residues: 220 loop : -0.85 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 116 TYR 0.013 0.001 TYR R 145 PHE 0.013 0.001 PHE B 234 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 9541) covalent geometry : angle 0.89628 (12921) SS BOND : bond 0.00089 ( 6) SS BOND : angle 1.69012 ( 12) hydrogen bonds : bond 0.24598 ( 455) hydrogen bonds : angle 7.55785 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.6105 time to fit residues: 85.1977 Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 209 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.0470 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 28 ASN R 113 GLN R 170 HIS B 6 GLN B 155 ASN B 230 ASN G 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133323 restraints weight = 10583.255| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.63 r_work: 0.3443 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9547 Z= 0.142 Angle : 0.534 7.544 12933 Z= 0.292 Chirality : 0.041 0.149 1420 Planarity : 0.004 0.045 1654 Dihedral : 4.304 31.090 1281 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.59 % Allowed : 9.94 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1155 helix: 2.09 (0.23), residues: 443 sheet: 0.26 (0.32), residues: 234 loop : -0.72 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.022 0.002 TYR R 145 PHE 0.018 0.002 PHE R 289 TRP 0.013 0.001 TRP P 25 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9541) covalent geometry : angle 0.53308 (12921) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.23900 ( 12) hydrogen bonds : bond 0.05601 ( 455) hydrogen bonds : angle 4.51793 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 31 PHE cc_start: 0.7792 (m-80) cc_final: 0.7521 (m-80) REVERT: R 117 ASP cc_start: 0.7042 (t0) cc_final: 0.5759 (p0) REVERT: B 59 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7526 (m-80) outliers start: 16 outliers final: 4 residues processed: 111 average time/residue: 0.6061 time to fit residues: 71.5530 Evaluate side-chains 91 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LYS Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 20 optimal weight: 0.4980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN A 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.181815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141304 restraints weight = 10704.484| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.10 r_work: 0.3463 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9547 Z= 0.103 Angle : 0.458 7.306 12933 Z= 0.248 Chirality : 0.039 0.147 1420 Planarity : 0.003 0.045 1654 Dihedral : 3.862 20.687 1279 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.79 % Allowed : 12.72 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1155 helix: 2.58 (0.23), residues: 450 sheet: 0.47 (0.32), residues: 230 loop : -0.72 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.021 0.001 TYR R 145 PHE 0.014 0.001 PHE A 222 TRP 0.014 0.001 TRP R 68 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9541) covalent geometry : angle 0.45778 (12921) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.91063 ( 12) hydrogen bonds : bond 0.04507 ( 455) hydrogen bonds : angle 4.04608 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 PHE cc_start: 0.7904 (m-80) cc_final: 0.7627 (m-80) REVERT: R 117 ASP cc_start: 0.7095 (t0) cc_final: 0.5718 (p0) REVERT: R 122 GLN cc_start: 0.5457 (mt0) cc_final: 0.4911 (pt0) REVERT: R 225 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7808 (mtt180) REVERT: B 59 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 138 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: N 53 GLN cc_start: 0.7789 (mp10) cc_final: 0.7556 (mp10) outliers start: 18 outliers final: 6 residues processed: 103 average time/residue: 0.5680 time to fit residues: 62.6052 Evaluate side-chains 90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LYS Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 2.9990 chunk 98 optimal weight: 0.0370 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138341 restraints weight = 10858.058| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.96 r_work: 0.3452 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9547 Z= 0.123 Angle : 0.477 10.368 12933 Z= 0.255 Chirality : 0.040 0.160 1420 Planarity : 0.004 0.045 1654 Dihedral : 3.925 20.600 1279 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.19 % Allowed : 13.42 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1155 helix: 2.50 (0.23), residues: 461 sheet: 0.55 (0.33), residues: 229 loop : -0.70 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.022 0.001 TYR R 145 PHE 0.016 0.001 PHE B 199 TRP 0.011 0.001 TRP R 241 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9541) covalent geometry : angle 0.47671 (12921) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.76082 ( 12) hydrogen bonds : bond 0.04439 ( 455) hydrogen bonds : angle 3.97410 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7030 (t0) cc_final: 0.5614 (p0) REVERT: R 122 GLN cc_start: 0.5487 (mt0) cc_final: 0.4963 (pt0) REVERT: R 225 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7867 (mtt180) REVERT: R 344 LYS cc_start: 0.5267 (mmtm) cc_final: 0.4626 (ttpt) REVERT: B 32 GLN cc_start: 0.8013 (pt0) cc_final: 0.7789 (pt0) REVERT: B 59 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: B 138 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 325 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: N 53 GLN cc_start: 0.7753 (mp10) cc_final: 0.7446 (mp10) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 0.5858 time to fit residues: 64.4298 Evaluate side-chains 98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 MET Chi-restraints excluded: chain R residue 64 LYS Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137907 restraints weight = 10821.351| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.99 r_work: 0.3441 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9547 Z= 0.119 Angle : 0.464 10.463 12933 Z= 0.249 Chirality : 0.039 0.146 1420 Planarity : 0.003 0.047 1654 Dihedral : 3.869 19.852 1279 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.09 % Allowed : 14.71 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1155 helix: 2.56 (0.24), residues: 462 sheet: 0.58 (0.33), residues: 229 loop : -0.76 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9541) covalent geometry : angle 0.46372 (12921) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.80067 ( 12) hydrogen bonds : bond 0.04250 ( 455) hydrogen bonds : angle 3.87277 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7064 (t0) cc_final: 0.5588 (p0) REVERT: R 122 GLN cc_start: 0.5489 (mt0) cc_final: 0.4943 (pt0) REVERT: R 225 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7890 (mtt180) REVERT: R 276 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7526 (mmp) REVERT: R 344 LYS cc_start: 0.5235 (mmtm) cc_final: 0.4197 (mttp) REVERT: B 32 GLN cc_start: 0.7866 (pt0) cc_final: 0.7566 (pt0) REVERT: B 59 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: B 138 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 325 MET cc_start: 0.8680 (ttm) cc_final: 0.8214 (mtm) REVERT: N 53 GLN cc_start: 0.7785 (mp10) cc_final: 0.7463 (mp10) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.6020 time to fit residues: 63.6233 Evaluate side-chains 96 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 MET Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137450 restraints weight = 10854.034| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.99 r_work: 0.3436 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9547 Z= 0.118 Angle : 0.463 11.127 12933 Z= 0.247 Chirality : 0.039 0.147 1420 Planarity : 0.003 0.047 1654 Dihedral : 3.855 19.870 1279 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.09 % Allowed : 15.61 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1155 helix: 2.60 (0.24), residues: 463 sheet: 0.54 (0.33), residues: 224 loop : -0.71 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE B 199 TRP 0.024 0.001 TRP R 68 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9541) covalent geometry : angle 0.46249 (12921) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.79219 ( 12) hydrogen bonds : bond 0.04186 ( 455) hydrogen bonds : angle 3.81818 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7148 (t0) cc_final: 0.5640 (p0) REVERT: R 122 GLN cc_start: 0.5519 (mt0) cc_final: 0.5093 (pt0) REVERT: R 225 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7910 (mtt180) REVERT: R 344 LYS cc_start: 0.5336 (mmtm) cc_final: 0.4142 (mttp) REVERT: B 32 GLN cc_start: 0.7907 (pt0) cc_final: 0.7623 (pt0) REVERT: B 59 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 138 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: B 220 GLN cc_start: 0.8400 (mt0) cc_final: 0.7899 (mt0) REVERT: N 53 GLN cc_start: 0.7779 (mp10) cc_final: 0.7512 (mp10) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.5528 time to fit residues: 58.6068 Evaluate side-chains 92 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135051 restraints weight = 10844.476| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.98 r_work: 0.3411 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9547 Z= 0.155 Angle : 0.498 11.400 12933 Z= 0.264 Chirality : 0.040 0.151 1420 Planarity : 0.003 0.047 1654 Dihedral : 3.995 20.791 1279 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.99 % Allowed : 16.30 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1155 helix: 2.49 (0.24), residues: 463 sheet: 0.45 (0.33), residues: 221 loop : -0.73 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 18 TYR 0.022 0.001 TYR R 145 PHE 0.017 0.002 PHE B 199 TRP 0.024 0.002 TRP R 68 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9541) covalent geometry : angle 0.49725 (12921) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.79685 ( 12) hydrogen bonds : bond 0.04542 ( 455) hydrogen bonds : angle 3.91180 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7150 (t0) cc_final: 0.5970 (p0) REVERT: R 122 GLN cc_start: 0.5684 (mt0) cc_final: 0.5290 (pt0) REVERT: R 225 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7932 (mtt180) REVERT: R 277 LEU cc_start: 0.8367 (tt) cc_final: 0.8047 (mt) REVERT: R 344 LYS cc_start: 0.5594 (mmtm) cc_final: 0.4348 (mttt) REVERT: B 59 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: B 138 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: B 325 MET cc_start: 0.8684 (ttm) cc_final: 0.8246 (mtm) REVERT: N 53 GLN cc_start: 0.7747 (mp10) cc_final: 0.7522 (mp10) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 0.5413 time to fit residues: 59.2467 Evaluate side-chains 90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 0.0570 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138345 restraints weight = 10763.298| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.98 r_work: 0.3444 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9547 Z= 0.103 Angle : 0.460 10.957 12933 Z= 0.246 Chirality : 0.039 0.145 1420 Planarity : 0.003 0.046 1654 Dihedral : 3.779 20.100 1279 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 17.30 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1155 helix: 2.64 (0.24), residues: 463 sheet: 0.48 (0.33), residues: 226 loop : -0.70 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.021 0.001 TYR R 145 PHE 0.012 0.001 PHE B 199 TRP 0.017 0.001 TRP R 68 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9541) covalent geometry : angle 0.45969 (12921) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.77683 ( 12) hydrogen bonds : bond 0.03986 ( 455) hydrogen bonds : angle 3.75196 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7076 (t0) cc_final: 0.5925 (p0) REVERT: R 122 GLN cc_start: 0.5644 (mt0) cc_final: 0.5279 (pt0) REVERT: R 225 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7869 (mtt180) REVERT: R 277 LEU cc_start: 0.8356 (tt) cc_final: 0.8015 (mt) REVERT: R 344 LYS cc_start: 0.5663 (mmtm) cc_final: 0.4472 (mttt) REVERT: B 59 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 138 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 220 GLN cc_start: 0.8392 (mt0) cc_final: 0.7908 (mt0) REVERT: N 53 GLN cc_start: 0.7732 (mp10) cc_final: 0.7489 (mp10) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.5705 time to fit residues: 58.7137 Evaluate side-chains 95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135659 restraints weight = 10757.112| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.99 r_work: 0.3408 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9547 Z= 0.142 Angle : 0.494 10.887 12933 Z= 0.264 Chirality : 0.040 0.155 1420 Planarity : 0.003 0.047 1654 Dihedral : 3.933 21.167 1279 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.89 % Allowed : 17.40 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1155 helix: 2.55 (0.24), residues: 464 sheet: 0.42 (0.33), residues: 223 loop : -0.73 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 308 TYR 0.022 0.001 TYR R 145 PHE 0.016 0.001 PHE B 199 TRP 0.015 0.001 TRP R 68 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9541) covalent geometry : angle 0.49328 (12921) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.78976 ( 12) hydrogen bonds : bond 0.04389 ( 455) hydrogen bonds : angle 3.86135 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7088 (t0) cc_final: 0.5920 (p0) REVERT: R 122 GLN cc_start: 0.5699 (mt0) cc_final: 0.5305 (pt0) REVERT: R 225 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7902 (mtt180) REVERT: R 277 LEU cc_start: 0.8366 (tt) cc_final: 0.8033 (mt) REVERT: R 344 LYS cc_start: 0.5560 (mmtm) cc_final: 0.4422 (mttt) REVERT: B 59 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: B 138 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: N 53 GLN cc_start: 0.7734 (mp10) cc_final: 0.7505 (mp10) outliers start: 19 outliers final: 11 residues processed: 91 average time/residue: 0.5591 time to fit residues: 54.5366 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 0.0270 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139848 restraints weight = 10703.091| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.99 r_work: 0.3462 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9547 Z= 0.095 Angle : 0.450 10.686 12933 Z= 0.241 Chirality : 0.038 0.147 1420 Planarity : 0.003 0.046 1654 Dihedral : 3.662 17.631 1279 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.09 % Allowed : 18.29 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1155 helix: 2.71 (0.24), residues: 464 sheet: 0.51 (0.33), residues: 227 loop : -0.67 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 308 TYR 0.020 0.001 TYR R 145 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9541) covalent geometry : angle 0.44989 (12921) SS BOND : bond 0.00119 ( 6) SS BOND : angle 0.75621 ( 12) hydrogen bonds : bond 0.03742 ( 455) hydrogen bonds : angle 3.65471 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: R 117 ASP cc_start: 0.7114 (t0) cc_final: 0.5918 (p0) REVERT: R 122 GLN cc_start: 0.5785 (mt0) cc_final: 0.5365 (pt0) REVERT: R 344 LYS cc_start: 0.5552 (mmtm) cc_final: 0.4452 (mttt) REVERT: A 309 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6791 (mm-30) REVERT: B 59 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: B 217 MET cc_start: 0.8390 (pmm) cc_final: 0.8143 (pmm) REVERT: B 220 GLN cc_start: 0.8407 (mt0) cc_final: 0.7982 (mt0) REVERT: B 325 MET cc_start: 0.8710 (ttm) cc_final: 0.8340 (mtm) REVERT: N 53 GLN cc_start: 0.7784 (mp10) cc_final: 0.7490 (mp10) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.5929 time to fit residues: 55.8715 Evaluate side-chains 78 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain N residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 0.0170 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.178941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138417 restraints weight = 10628.723| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.98 r_work: 0.3456 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9547 Z= 0.101 Angle : 0.462 11.797 12933 Z= 0.247 Chirality : 0.039 0.144 1420 Planarity : 0.003 0.047 1654 Dihedral : 3.645 18.633 1279 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.89 % Allowed : 18.89 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1155 helix: 2.76 (0.24), residues: 463 sheet: 0.46 (0.33), residues: 229 loop : -0.63 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 225 TYR 0.021 0.001 TYR R 145 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9541) covalent geometry : angle 0.46113 (12921) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.77695 ( 12) hydrogen bonds : bond 0.03773 ( 455) hydrogen bonds : angle 3.65659 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.83 seconds wall clock time: 55 minutes 47.59 seconds (3347.59 seconds total)