Starting phenix.real_space_refine on Wed Aug 5 09:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zx_67439/08_2026/20zx_67439.map" } resolution = 2.96 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= 0.016 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 57 5.16 5 C 5760 2.51 5 N 1596 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9077 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2395 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UBL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 9077 At special positions: 0 Unit cell: (102.93, 118.26, 133.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 1 15.00 O 1663 8.00 N 1596 7.00 C 5760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.04 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 0.84 Conformation dependent library (CDL) restraints added in 331.3 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 10 through 23 removed outlier: 3.675A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'G' and resid 9 through 11 No H-bonds generated for 'chain 'G' and resid 9 through 11' Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.900A pdb=" N GLU G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 18 through 50 Proline residue: R 38 - end of helix Processing helix chain 'R' and resid 55 through 74 removed outlier: 3.616A pdb=" N TYR R 60 " --> pdb=" O VAL R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 85 removed outlier: 3.964A pdb=" N ARG R 78 " --> pdb=" O SER R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 124 removed outlier: 3.525A pdb=" N CYS R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 removed outlier: 3.955A pdb=" N ARG R 130 " --> pdb=" O LEU R 127 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS R 131 " --> pdb=" O ARG R 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 127 through 131' Processing helix chain 'R' and resid 134 through 160 removed outlier: 3.957A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Proline residue: R 155 - end of helix Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 188 through 199 Processing helix chain 'R' and resid 200 through 219 Processing helix chain 'R' and resid 226 through 247 Processing helix chain 'R' and resid 247 through 262 Processing helix chain 'R' and resid 268 through 288 removed outlier: 3.933A pdb=" N LEU R 284 " --> pdb=" O MET R 280 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 285 " --> pdb=" O VAL R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 298 Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 306 Processing helix chain 'R' and resid 306 through 311 removed outlier: 3.659A pdb=" N LEU R 311 " --> pdb=" O THR R 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.700A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.727A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.592A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.710A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 357 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.162A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.640A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.782A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.670A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.825A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.588A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.703A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 282 through 283 removed outlier: 6.634A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.570A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.918A pdb=" N GLY E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 39 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 147 removed outlier: 6.760A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1209 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: 1.53 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1456 1.31 - 1.44: 2565 1.44 - 1.57: 5163 1.57 - 1.70: 2 1.70 - 1.83: 82 Bond restraints: 9268 Sorted by residual: bond pdb=" CAS UBL R 401 " pdb=" CAT UBL R 401 " ideal model delta sigma weight residual 1.333 1.518 -0.185 2.00e-02 2.50e+03 8.58e+01 bond pdb=" OAA UBL R 401 " pdb=" PAC UBL R 401 " ideal model delta sigma weight residual 1.522 1.639 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" OAF UBL R 401 " pdb=" PAC UBL R 401 " ideal model delta sigma weight residual 1.727 1.623 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" OAB UBL R 401 " pdb=" PAC UBL R 401 " ideal model delta sigma weight residual 1.528 1.444 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O1 UBL R 401 " pdb=" PAC UBL R 401 " ideal model delta sigma weight residual 1.526 1.448 0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 9263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 12518 4.04 - 8.09: 35 8.09 - 12.13: 4 12.13 - 16.17: 0 16.17 - 20.22: 2 Bond angle restraints: 12559 Sorted by residual: angle pdb=" CAR UBL R 401 " pdb=" CAS UBL R 401 " pdb=" CAT UBL R 401 " ideal model delta sigma weight residual 127.71 107.49 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" CAS UBL R 401 " pdb=" CAT UBL R 401 " pdb=" CAU UBL R 401 " ideal model delta sigma weight residual 127.34 107.90 19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O1 UBL R 401 " pdb=" PAC UBL R 401 " pdb=" OAB UBL R 401 " ideal model delta sigma weight residual 114.01 102.50 11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" OAA UBL R 401 " pdb=" PAC UBL R 401 " pdb=" OAF UBL R 401 " ideal model delta sigma weight residual 100.39 111.19 -10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA ARG R 49 " pdb=" C ARG R 49 " pdb=" O ARG R 49 " ideal model delta sigma weight residual 118.69 114.94 3.75 1.15e+00 7.56e-01 1.06e+01 ... (remaining 12554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.93: 5013 18.93 - 37.85: 433 37.85 - 56.78: 82 56.78 - 75.70: 23 75.70 - 94.63: 8 Dihedral angle restraints: 5559 sinusoidal: 2218 harmonic: 3341 Sorted by residual: dihedral pdb=" CA GLU R 177 " pdb=" C GLU R 177 " pdb=" N SER R 178 " pdb=" CA SER R 178 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP B 87 " pdb=" C TRP B 87 " pdb=" N ASP B 88 " pdb=" CA ASP B 88 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 296 " pdb=" C ASP B 296 " pdb=" N PHE B 297 " pdb=" CA PHE B 297 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 893 0.030 - 0.061: 355 0.061 - 0.091: 88 0.091 - 0.121: 66 0.121 - 0.151: 11 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA VAL R 12 " pdb=" N VAL R 12 " pdb=" C VAL R 12 " pdb=" CB VAL R 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1410 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAR UBL R 401 " -0.073 2.00e-02 2.50e+03 7.34e-02 5.38e+01 pdb=" CAS UBL R 401 " 0.073 2.00e-02 2.50e+03 pdb=" CAT UBL R 401 " 0.074 2.00e-02 2.50e+03 pdb=" CAU UBL R 401 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 49 " 0.269 9.50e-02 1.11e+02 1.21e-01 8.96e+00 pdb=" NE ARG R 49 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG R 49 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 49 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 49 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 128 " -0.175 9.50e-02 1.11e+02 7.86e-02 3.89e+00 pdb=" NE ARG R 128 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG R 128 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 128 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 128 " -0.004 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1924 2.78 - 3.31: 8861 3.31 - 3.84: 15023 3.84 - 4.37: 18709 4.37 - 4.90: 31806 Nonbonded interactions: 76323 Sorted by model distance: nonbonded pdb=" O ASP A 229 " pdb=" OD1 ASP A 229 " model vdw 2.253 3.040 nonbonded pdb=" O LYS G 31 " pdb=" OD1 ASP G 35 " model vdw 2.296 3.040 nonbonded pdb=" O ASP B 81 " pdb=" OD1 ASP B 81 " model vdw 2.399 3.040 nonbonded pdb=" O LYS B 20 " pdb=" O ILE B 23 " model vdw 2.430 3.040 nonbonded pdb=" O ASP B 338 " pdb=" OG SER B 339 " model vdw 2.438 3.040 ... (remaining 76318 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.004 0.185 9273 Z= 0.197 Angle : 0.636 20.217 12569 Z= 0.300 Chirality : 0.040 0.151 1413 Planarity : 0.006 0.121 1602 Dihedral : 15.345 94.629 3388 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.71 % Allowed : 12.64 % Favored : 86.65 % 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: 0.27 (0.26), residues: 1135 helix: 1.76 (0.27), residues: 392 sheet: -1.03 (0.31), residues: 272 loop : -0.30 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 247 TYR 0.012 0.001 TYR E 235 PHE 0.009 0.001 PHE B 156 TRP 0.016 0.001 TRP B 104 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 ( 9268) covalent geometry : angle 0.63536 / 0.30 (12559) SS BOND : bond 0.00590 / 0.31 ( 5) SS BOND : angle 1.35418 / 0.72 ( 10) hydrogen bonds : bond 0.15764 / 10.83 ( 428) hydrogen bonds : angle 7.30068 / 5.16 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: G 31 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6858 (tmtm) REVERT: R 92 LEU cc_start: 0.7617 (mt) cc_final: 0.7383 (pp) REVERT: A 310 LYS cc_start: 0.7714 (tmtt) cc_final: 0.6672 (ttmm) REVERT: A 314 ASP cc_start: 0.7701 (m-30) cc_final: 0.7374 (m-30) REVERT: E 5 GLU cc_start: 0.7260 (mp0) cc_final: 0.7054 (mp0) REVERT: E 140 MET cc_start: 0.8105 (tpt) cc_final: 0.7395 (mmt) REVERT: E 235 TYR cc_start: 0.5059 (OUTLIER) cc_final: 0.4810 (m-80) outliers start: 7 outliers final: 2 residues processed: 131 average time/residue: 0.5581 time to fit residues: 77.6857 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain E residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 HIS R 289 ASN E 81 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.127075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103305 restraints weight = 15191.650| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.94 r_work: 0.3276 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9273 Z= 0.140 Angle : 0.563 7.007 12569 Z= 0.292 Chirality : 0.043 0.215 1413 Planarity : 0.004 0.043 1602 Dihedral : 7.318 70.455 1309 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.83 % Allowed : 12.13 % Favored : 86.03 % 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: 0.54 (0.26), residues: 1135 helix: 1.86 (0.27), residues: 392 sheet: -0.67 (0.31), residues: 283 loop : -0.16 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.015 0.001 TYR E 235 PHE 0.013 0.001 PHE B 156 TRP 0.018 0.002 TRP B 344 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9268) covalent geometry : angle 0.56122 / 0.29 (12559) SS BOND : bond 0.00789 / 0.42 ( 5) SS BOND : angle 1.50986 / 0.83 ( 10) hydrogen bonds : bond 0.03773 / 2.59 ( 428) hydrogen bonds : angle 5.40089 / 3.86 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7502 (mt) cc_final: 0.7119 (pp) REVERT: A 278 TYR cc_start: 0.6234 (m-80) cc_final: 0.5777 (m-80) REVERT: A 281 GLU cc_start: 0.6462 (tp30) cc_final: 0.6234 (tp30) REVERT: A 310 LYS cc_start: 0.7919 (tmtt) cc_final: 0.6844 (ttmm) REVERT: A 314 ASP cc_start: 0.8031 (m-30) cc_final: 0.7687 (m-30) REVERT: E 116 LEU cc_start: 0.8576 (tp) cc_final: 0.8217 (tp) REVERT: E 140 MET cc_start: 0.7845 (tpt) cc_final: 0.7136 (mmt) outliers start: 18 outliers final: 8 residues processed: 139 average time/residue: 0.5561 time to fit residues: 82.5950 Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.123153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098194 restraints weight = 15164.695| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.04 r_work: 0.3181 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9273 Z= 0.302 Angle : 0.679 10.265 12569 Z= 0.352 Chirality : 0.048 0.260 1413 Planarity : 0.005 0.040 1602 Dihedral : 7.326 67.376 1303 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.77 % Allowed : 12.13 % Favored : 84.10 % 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: 0.27 (0.26), residues: 1135 helix: 1.40 (0.26), residues: 391 sheet: -0.49 (0.30), residues: 296 loop : -0.30 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.016 0.002 TYR E 235 PHE 0.017 0.002 PHE B 156 TRP 0.020 0.002 TRP B 87 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.30 ( 9268) covalent geometry : angle 0.67562 / 0.35 (12559) SS BOND : bond 0.01436 / 0.75 ( 5) SS BOND : angle 2.50073 / 1.34 ( 10) hydrogen bonds : bond 0.04446 / 3.04 ( 428) hydrogen bonds : angle 5.56442 / 3.98 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.367 Fit side-chains REVERT: R 23 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6649 (ppt90) REVERT: R 92 LEU cc_start: 0.7424 (mt) cc_final: 0.6983 (pp) REVERT: A 278 TYR cc_start: 0.6171 (m-80) cc_final: 0.5701 (m-80) REVERT: A 310 LYS cc_start: 0.8131 (tttt) cc_final: 0.7524 (ttmm) REVERT: E 116 LEU cc_start: 0.8619 (tp) cc_final: 0.8233 (tp) REVERT: E 140 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7275 (mmt) outliers start: 37 outliers final: 21 residues processed: 142 average time/residue: 0.6045 time to fit residues: 91.2736 Evaluate side-chains 141 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN R 116 ASN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102394 restraints weight = 15539.398| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3242 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9273 Z= 0.143 Angle : 0.556 6.917 12569 Z= 0.290 Chirality : 0.042 0.223 1413 Planarity : 0.004 0.043 1602 Dihedral : 6.868 69.027 1303 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.75 % Allowed : 14.37 % Favored : 82.87 % 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: 0.48 (0.26), residues: 1135 helix: 1.66 (0.27), residues: 394 sheet: -0.38 (0.30), residues: 294 loop : -0.29 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.014 0.001 TYR A 358 PHE 0.013 0.001 PHE B 156 TRP 0.019 0.002 TRP B 344 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9268) covalent geometry : angle 0.55428 / 0.29 (12559) SS BOND : bond 0.00785 / 0.41 ( 5) SS BOND : angle 1.59790 / 0.85 ( 10) hydrogen bonds : bond 0.03636 / 2.48 ( 428) hydrogen bonds : angle 5.14865 / 3.68 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: R 23 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6570 (ppt90) REVERT: R 92 LEU cc_start: 0.7408 (mt) cc_final: 0.6918 (pp) REVERT: A 278 TYR cc_start: 0.6227 (m-80) cc_final: 0.5772 (m-80) REVERT: A 284 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6397 (mtm-85) REVERT: A 310 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7512 (ttmm) REVERT: E 116 LEU cc_start: 0.8555 (tp) cc_final: 0.8207 (tp) REVERT: E 140 MET cc_start: 0.7790 (tpt) cc_final: 0.7130 (mmt) REVERT: E 215 THR cc_start: 0.7501 (p) cc_final: 0.7119 (t) outliers start: 27 outliers final: 18 residues processed: 141 average time/residue: 0.5406 time to fit residues: 81.3116 Evaluate side-chains 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 ASN B 225 GLN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101083 restraints weight = 15289.746| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.95 r_work: 0.3234 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9273 Z= 0.179 Angle : 0.578 8.040 12569 Z= 0.302 Chirality : 0.043 0.219 1413 Planarity : 0.004 0.046 1602 Dihedral : 6.661 69.099 1301 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.16 % Allowed : 14.98 % Favored : 81.86 % 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: 0.47 (0.26), residues: 1135 helix: 1.63 (0.26), residues: 394 sheet: -0.33 (0.30), residues: 295 loop : -0.30 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.017 0.002 TYR A 230 PHE 0.013 0.002 PHE B 156 TRP 0.019 0.002 TRP B 344 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 9268) covalent geometry : angle 0.57602 / 0.30 (12559) SS BOND : bond 0.00986 / 0.52 ( 5) SS BOND : angle 1.83999 / 0.98 ( 10) hydrogen bonds : bond 0.03726 / 2.54 ( 428) hydrogen bonds : angle 5.14042 / 3.68 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.354 Fit side-chains REVERT: R 23 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6594 (ppt90) REVERT: R 92 LEU cc_start: 0.7417 (mt) cc_final: 0.6879 (pp) REVERT: A 278 TYR cc_start: 0.6206 (m-80) cc_final: 0.5761 (m-80) REVERT: A 284 ARG cc_start: 0.6735 (ttp-170) cc_final: 0.6510 (mtm-85) REVERT: A 310 LYS cc_start: 0.7994 (tttt) cc_final: 0.7557 (ttmm) REVERT: E 116 LEU cc_start: 0.8542 (tp) cc_final: 0.8189 (tp) REVERT: E 140 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7270 (mmt) REVERT: E 215 THR cc_start: 0.7486 (p) cc_final: 0.7120 (t) outliers start: 31 outliers final: 18 residues processed: 144 average time/residue: 0.5587 time to fit residues: 85.9851 Evaluate side-chains 138 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102668 restraints weight = 15365.375| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.90 r_work: 0.3274 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.123 Angle : 0.540 7.227 12569 Z= 0.281 Chirality : 0.042 0.184 1413 Planarity : 0.004 0.046 1602 Dihedral : 6.353 68.756 1301 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 15.90 % Favored : 81.45 % 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: 0.62 (0.26), residues: 1135 helix: 1.82 (0.26), residues: 394 sheet: -0.31 (0.30), residues: 297 loop : -0.24 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 247 TYR 0.013 0.001 TYR A 358 PHE 0.011 0.001 PHE B 156 TRP 0.019 0.002 TRP B 344 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9268) covalent geometry : angle 0.53900 / 0.28 (12559) SS BOND : bond 0.00671 / 0.35 ( 5) SS BOND : angle 1.39668 / 0.74 ( 10) hydrogen bonds : bond 0.03389 / 2.30 ( 428) hydrogen bonds : angle 4.92399 / 3.53 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.309 Fit side-chains REVERT: R 92 LEU cc_start: 0.7468 (mt) cc_final: 0.6902 (pp) REVERT: A 278 TYR cc_start: 0.6091 (m-80) cc_final: 0.5699 (m-80) REVERT: A 284 ARG cc_start: 0.6864 (ttp-170) cc_final: 0.6397 (mtm-85) REVERT: A 310 LYS cc_start: 0.7967 (tttt) cc_final: 0.6885 (ttmt) REVERT: A 314 ASP cc_start: 0.8083 (m-30) cc_final: 0.7776 (m-30) REVERT: E 116 LEU cc_start: 0.8493 (tp) cc_final: 0.8158 (tp) REVERT: E 140 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7261 (mmt) REVERT: E 215 THR cc_start: 0.7477 (p) cc_final: 0.7115 (t) outliers start: 26 outliers final: 15 residues processed: 150 average time/residue: 0.4957 time to fit residues: 79.1172 Evaluate side-chains 141 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 9.9990 chunk 103 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 22 GLN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102904 restraints weight = 15359.581| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.97 r_work: 0.3275 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9273 Z= 0.127 Angle : 0.545 7.037 12569 Z= 0.283 Chirality : 0.041 0.172 1413 Planarity : 0.004 0.055 1602 Dihedral : 6.232 66.888 1301 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.75 % Allowed : 16.62 % Favored : 80.63 % 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: 0.73 (0.26), residues: 1135 helix: 1.94 (0.26), residues: 391 sheet: -0.21 (0.30), residues: 296 loop : -0.22 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 247 TYR 0.014 0.001 TYR A 358 PHE 0.010 0.001 PHE A 189 TRP 0.019 0.001 TRP B 344 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9268) covalent geometry : angle 0.54408 / 0.28 (12559) SS BOND : bond 0.00716 / 0.38 ( 5) SS BOND : angle 1.46358 / 0.78 ( 10) hydrogen bonds : bond 0.03348 / 2.28 ( 428) hydrogen bonds : angle 4.86937 / 3.50 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.451 Fit side-chains REVERT: R 23 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6663 (ppt90) REVERT: R 92 LEU cc_start: 0.7462 (mt) cc_final: 0.6864 (pp) REVERT: A 278 TYR cc_start: 0.6115 (m-80) cc_final: 0.5728 (m-80) REVERT: A 310 LYS cc_start: 0.7911 (tttt) cc_final: 0.6833 (ttmt) REVERT: A 314 ASP cc_start: 0.8130 (m-30) cc_final: 0.7837 (m-30) REVERT: E 116 LEU cc_start: 0.8505 (tp) cc_final: 0.8175 (tp) REVERT: E 140 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7275 (mmt) REVERT: E 215 THR cc_start: 0.7459 (p) cc_final: 0.7106 (t) outliers start: 27 outliers final: 19 residues processed: 150 average time/residue: 0.4886 time to fit residues: 78.5883 Evaluate side-chains 144 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 22 GLN A 261 GLN E 81 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101275 restraints weight = 15293.729| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.95 r_work: 0.3237 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9273 Z= 0.190 Angle : 0.586 8.091 12569 Z= 0.303 Chirality : 0.043 0.190 1413 Planarity : 0.005 0.050 1602 Dihedral : 6.486 65.248 1301 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.96 % Allowed : 16.82 % 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: 0.64 (0.26), residues: 1135 helix: 1.79 (0.26), residues: 393 sheet: -0.25 (0.30), residues: 299 loop : -0.22 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 247 TYR 0.017 0.002 TYR A 358 PHE 0.012 0.002 PHE B 156 TRP 0.019 0.002 TRP B 344 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 9268) covalent geometry : angle 0.58349 / 0.30 (12559) SS BOND : bond 0.01025 / 0.54 ( 5) SS BOND : angle 1.88087 / 1.00 ( 10) hydrogen bonds : bond 0.03658 / 2.49 ( 428) hydrogen bonds : angle 5.01833 / 3.60 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.345 Fit side-chains REVERT: R 23 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6630 (ppt90) REVERT: R 84 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7299 (mm) REVERT: R 92 LEU cc_start: 0.7454 (mt) cc_final: 0.6845 (pp) REVERT: A 278 TYR cc_start: 0.6127 (m-80) cc_final: 0.5723 (m-80) REVERT: A 310 LYS cc_start: 0.8035 (tttt) cc_final: 0.7529 (ttmm) REVERT: E 116 LEU cc_start: 0.8539 (tp) cc_final: 0.8217 (tp) REVERT: E 140 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7391 (mmt) REVERT: E 215 THR cc_start: 0.7498 (p) cc_final: 0.7132 (t) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.5078 time to fit residues: 79.0711 Evaluate side-chains 144 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 0.0000 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 22 GLN A 261 GLN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105461 restraints weight = 15402.361| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.94 r_work: 0.3269 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9273 Z= 0.135 Angle : 0.558 7.092 12569 Z= 0.290 Chirality : 0.042 0.168 1413 Planarity : 0.004 0.053 1602 Dihedral : 6.384 65.110 1301 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 17.43 % Favored : 79.92 % 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: 0.73 (0.26), residues: 1135 helix: 1.88 (0.26), residues: 393 sheet: -0.11 (0.30), residues: 296 loop : -0.25 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 247 TYR 0.016 0.001 TYR A 358 PHE 0.010 0.001 PHE A 189 TRP 0.019 0.002 TRP B 344 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9268) covalent geometry : angle 0.55636 / 0.29 (12559) SS BOND : bond 0.00755 / 0.40 ( 5) SS BOND : angle 1.50481 / 0.80 ( 10) hydrogen bonds : bond 0.03408 / 2.32 ( 428) hydrogen bonds : angle 4.89841 / 3.52 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.347 Fit side-chains REVERT: R 23 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6629 (ppt90) REVERT: R 84 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7285 (mm) REVERT: R 92 LEU cc_start: 0.7456 (mt) cc_final: 0.6836 (pp) REVERT: A 278 TYR cc_start: 0.6113 (m-80) cc_final: 0.5732 (m-80) REVERT: A 310 LYS cc_start: 0.7944 (tttt) cc_final: 0.7481 (ttmm) REVERT: E 116 LEU cc_start: 0.8522 (tp) cc_final: 0.8193 (tp) REVERT: E 140 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7186 (mmt) REVERT: E 215 THR cc_start: 0.7445 (p) cc_final: 0.7127 (t) outliers start: 26 outliers final: 20 residues processed: 139 average time/residue: 0.4634 time to fit residues: 68.8817 Evaluate side-chains 139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 22 GLN A 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101699 restraints weight = 15189.903| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9273 Z= 0.167 Angle : 0.578 8.095 12569 Z= 0.299 Chirality : 0.043 0.173 1413 Planarity : 0.005 0.048 1602 Dihedral : 6.524 69.786 1301 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.55 % Allowed : 17.53 % Favored : 79.92 % 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: 0.68 (0.26), residues: 1135 helix: 1.83 (0.26), residues: 393 sheet: -0.12 (0.30), residues: 296 loop : -0.29 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 247 TYR 0.017 0.002 TYR A 358 PHE 0.012 0.002 PHE R 152 TRP 0.019 0.002 TRP B 344 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9268) covalent geometry : angle 0.57626 / 0.30 (12559) SS BOND : bond 0.00931 / 0.49 ( 5) SS BOND : angle 1.77751 / 0.94 ( 10) hydrogen bonds : bond 0.03543 / 2.41 ( 428) hydrogen bonds : angle 4.95536 / 3.56 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.371 Fit side-chains REVERT: R 23 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6636 (ppt90) REVERT: R 84 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7283 (mm) REVERT: R 92 LEU cc_start: 0.7425 (mt) cc_final: 0.6813 (pp) REVERT: A 278 TYR cc_start: 0.6088 (m-80) cc_final: 0.5695 (m-80) REVERT: A 310 LYS cc_start: 0.7995 (tttt) cc_final: 0.7500 (ttmm) REVERT: E 140 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7295 (mmt) REVERT: E 215 THR cc_start: 0.7459 (p) cc_final: 0.7114 (t) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.4994 time to fit residues: 75.8560 Evaluate side-chains 146 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN A 22 GLN A 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105689 restraints weight = 15254.007| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.93 r_work: 0.3267 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9273 Z= 0.134 Angle : 0.562 8.205 12569 Z= 0.290 Chirality : 0.042 0.162 1413 Planarity : 0.004 0.047 1602 Dihedral : 6.447 72.718 1301 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.65 % Allowed : 17.64 % Favored : 79.71 % 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: 0.73 (0.26), residues: 1135 helix: 1.95 (0.26), residues: 391 sheet: -0.15 (0.30), residues: 299 loop : -0.29 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 247 TYR 0.016 0.001 TYR A 358 PHE 0.010 0.001 PHE B 156 TRP 0.019 0.002 TRP B 344 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9268) covalent geometry : angle 0.56075 / 0.29 (12559) SS BOND : bond 0.00757 / 0.40 ( 5) SS BOND : angle 1.54099 / 0.82 ( 10) hydrogen bonds : bond 0.03384 / 2.30 ( 428) hydrogen bonds : angle 4.85839 / 3.50 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.93 seconds wall clock time: 58 minutes 30.25 seconds (3510.25 seconds total)