Starting phenix.real_space_refine on Thu Jul 2 13:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wrb_37771/07_2026/8wrb_37771.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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 65 5.16 5 C 5646 2.51 5 N 1484 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2195 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'UBL': 1} Inner-chain residues flagged as termini: ['pdbres="SER R 602 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.15 Number of scatterers: 8842 At special positions: 0 Unit cell: (89.88, 116.63, 125.19, 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 65 16.00 P 1 15.00 O 1646 8.00 N 1484 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 348.3 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 39.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.516A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.502A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.030A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.502A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.500A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.370A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.541A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 81 removed outlier: 3.649A pdb=" N THR R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 116 removed outlier: 3.526A pdb=" N LEU R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.613A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 197 removed outlier: 4.086A pdb=" N LYS R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 3.788A pdb=" N LYS R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 295 removed outlier: 3.965A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.051A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 318 Processing helix chain 'R' and resid 318 through 331 Proline residue: R 324 - end of helix removed outlier: 3.568A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.751A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.639A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.582A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.884A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.324A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.454A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.776A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.834A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.446A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.131A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1353 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: 0.93 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1421 1.31 - 1.44: 2500 1.44 - 1.56: 5005 1.56 - 1.69: 1 1.69 - 1.82: 95 Bond restraints: 9022 Sorted by residual: bond pdb=" CAK UBL R 603 " pdb=" OAJ UBL R 603 " ideal model delta sigma weight residual 1.326 1.414 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CAR UBL R 603 " pdb=" CAS UBL R 603 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" OAF UBL R 603 " pdb=" PAC UBL R 603 " ideal model delta sigma weight residual 1.727 1.668 0.059 2.00e-02 2.50e+03 8.76e+00 bond pdb=" CAT UBL R 603 " pdb=" CAU UBL R 603 " ideal model delta sigma weight residual 1.498 1.555 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" CAH UBL R 603 " pdb=" CAI UBL R 603 " ideal model delta sigma weight residual 1.510 1.552 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 12214 4.77 - 9.53: 7 9.53 - 14.30: 0 14.30 - 19.06: 1 19.06 - 23.83: 1 Bond angle restraints: 12223 Sorted by residual: angle pdb=" CAR UBL R 603 " pdb=" CAS UBL R 603 " pdb=" CAT UBL R 603 " ideal model delta sigma weight residual 127.71 151.54 -23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" CAS UBL R 603 " pdb=" CAT UBL R 603 " pdb=" CAU UBL R 603 " ideal model delta sigma weight residual 127.34 111.16 16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" OAA UBL R 603 " pdb=" PAC UBL R 603 " pdb=" OAF UBL R 603 " ideal model delta sigma weight residual 100.39 109.68 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CAL UBL R 603 " pdb=" CAK UBL R 603 " pdb=" OAJ UBL R 603 " ideal model delta sigma weight residual 111.99 120.05 -8.06 3.00e+00 1.11e-01 7.21e+00 angle pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C20 CLR R 601 " ideal model delta sigma weight residual 119.60 112.88 6.72 3.00e+00 1.11e-01 5.02e+00 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.61: 5177 19.61 - 39.21: 123 39.21 - 58.82: 23 58.82 - 78.43: 5 78.43 - 98.03: 2 Dihedral angle restraints: 5330 sinusoidal: 2038 harmonic: 3292 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CAI UBL R 603 " pdb=" CAK UBL R 603 " pdb=" OAJ UBL R 603 " pdb=" CAL UBL R 603 " ideal model delta sinusoidal sigma weight residual 174.85 -87.12 -98.03 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 5327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1326 0.089 - 0.178: 74 0.178 - 0.266: 0 0.266 - 0.355: 2 0.355 - 0.444: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C10 CLR R 601 " pdb=" C1 CLR R 601 " pdb=" C5 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.51 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C17 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C16 CLR R 601 " pdb=" C20 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1400 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 323 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO R 324 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO R 256 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.018 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1069 2.75 - 3.29: 8454 3.29 - 3.83: 14738 3.83 - 4.36: 18178 4.36 - 4.90: 31679 Nonbonded interactions: 74118 Sorted by model distance: nonbonded pdb=" OD1 ASP A 341 " pdb=" OH TYR R 261 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.269 3.040 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" O SER A 281 " model vdw 2.296 3.040 ... (remaining 74113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9026 Z= 0.168 Angle : 0.487 23.827 12229 Z= 0.221 Chirality : 0.042 0.444 1403 Planarity : 0.003 0.039 1532 Dihedral : 9.479 98.032 3199 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.06 % Allowed : 1.90 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.02 (0.24), residues: 1118 helix: 1.36 (0.25), residues: 411 sheet: 0.72 (0.29), residues: 293 loop : 0.09 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.009 0.001 TYR E 190 PHE 0.007 0.001 PHE A 189 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9022) covalent geometry : angle 0.48740 / 0.22 (12223) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 0.55088 / 0.32 ( 6) hydrogen bonds : bond 0.23783 / 15.60 ( 477) hydrogen bonds : angle 7.08183 / 4.97 ( 1353) Misc. bond : bond 0.10330 / 5.44 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8030 (tp30) cc_final: 0.6952 (tt0) REVERT: A 208 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7181 (ttp80) REVERT: A 251 ASP cc_start: 0.8388 (t70) cc_final: 0.8004 (t0) REVERT: A 275 GLU cc_start: 0.8175 (tt0) cc_final: 0.7890 (mt-10) REVERT: A 308 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 330 LYS cc_start: 0.7731 (mttt) cc_final: 0.7440 (mttm) REVERT: A 354 PHE cc_start: 0.8219 (t80) cc_final: 0.7423 (t80) REVERT: B 23 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7828 (tptm) REVERT: B 42 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7677 (ttm-80) REVERT: B 46 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7571 (mtp-110) REVERT: B 219 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7268 (mmm160) REVERT: B 226 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 259 GLN cc_start: 0.8534 (pt0) cc_final: 0.8101 (pt0) REVERT: E 83 MET cc_start: 0.8869 (mtm) cc_final: 0.8572 (mtp) REVERT: E 160 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6687 (mtp85) REVERT: E 213 THR cc_start: 0.7949 (m) cc_final: 0.7605 (p) REVERT: E 218 ARG cc_start: 0.7236 (mpp-170) cc_final: 0.6913 (mtt90) REVERT: R 64 ILE cc_start: 0.7775 (mt) cc_final: 0.7550 (mp) REVERT: R 180 MET cc_start: 0.7656 (mmm) cc_final: 0.7098 (mpt) REVERT: R 203 MET cc_start: 0.8056 (ptp) cc_final: 0.7846 (ptm) REVERT: R 288 ILE cc_start: 0.8408 (mt) cc_final: 0.8199 (mp) REVERT: R 326 MET cc_start: 0.7663 (ttp) cc_final: 0.7346 (ttm) outliers start: 10 outliers final: 9 residues processed: 197 average time/residue: 0.4168 time to fit residues: 88.2900 Evaluate side-chains 145 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 602 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 322 HIS B 91 HIS E 113 GLN E 183 GLN R 83 HIS R 199 HIS R 206 HIS R 293 GLN R 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102164 restraints weight = 10428.658| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.24 r_work: 0.2959 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9026 Z= 0.125 Angle : 0.489 5.743 12229 Z= 0.270 Chirality : 0.041 0.153 1403 Planarity : 0.004 0.039 1532 Dihedral : 6.153 59.635 1274 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.64 % Allowed : 8.87 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.91 (0.25), residues: 1118 helix: 2.79 (0.24), residues: 407 sheet: 0.89 (0.30), residues: 275 loop : 0.08 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.018 0.001 TYR R 92 PHE 0.015 0.001 PHE R 227 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9022) covalent geometry : angle 0.48926 / 0.27 (12223) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 0.84324 / 0.48 ( 6) hydrogen bonds : bond 0.04716 / 3.13 ( 477) hydrogen bonds : angle 4.56668 / 3.24 ( 1353) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.236 Fit side-chains REVERT: A 29 LYS cc_start: 0.8234 (tttt) cc_final: 0.8024 (ttpp) REVERT: A 186 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8352 (mt-10) REVERT: A 251 ASP cc_start: 0.8295 (t70) cc_final: 0.7882 (t0) REVERT: A 330 LYS cc_start: 0.7635 (mttt) cc_final: 0.7355 (mttm) REVERT: A 354 PHE cc_start: 0.8340 (t80) cc_final: 0.7585 (t80) REVERT: B 42 ARG cc_start: 0.8274 (ttt90) cc_final: 0.7888 (ttm-80) REVERT: B 46 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7790 (mtp-110) REVERT: B 170 ASP cc_start: 0.7907 (t70) cc_final: 0.7456 (t70) REVERT: B 198 LEU cc_start: 0.8464 (mt) cc_final: 0.8209 (mt) REVERT: B 219 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7495 (mmm160) REVERT: B 234 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: B 259 GLN cc_start: 0.8688 (pt0) cc_final: 0.8316 (pt0) REVERT: B 262 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8408 (ttm) REVERT: E 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8286 (tt0) REVERT: E 83 MET cc_start: 0.8850 (mtm) cc_final: 0.8634 (mtp) REVERT: E 160 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.6863 (mtp85) REVERT: E 186 GLN cc_start: 0.8050 (tt0) cc_final: 0.7686 (pt0) REVERT: E 213 THR cc_start: 0.8210 (m) cc_final: 0.7925 (p) REVERT: E 218 ARG cc_start: 0.7231 (mpp-170) cc_final: 0.6849 (mtt90) REVERT: E 223 ASP cc_start: 0.6746 (m-30) cc_final: 0.6508 (m-30) REVERT: E 234 GLU cc_start: 0.8768 (pt0) cc_final: 0.8562 (pt0) REVERT: R 63 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8169 (p) REVERT: R 127 CYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7247 (t) REVERT: R 326 MET cc_start: 0.7398 (ttp) cc_final: 0.7124 (ttm) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 0.4455 time to fit residues: 84.5609 Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN E 113 GLN R 90 GLN R 199 HIS R 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102286 restraints weight = 10344.278| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.20 r_work: 0.2969 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9026 Z= 0.112 Angle : 0.460 6.736 12229 Z= 0.251 Chirality : 0.041 0.144 1403 Planarity : 0.003 0.039 1532 Dihedral : 5.442 51.859 1267 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.06 % Allowed : 10.77 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.07 (0.25), residues: 1118 helix: 3.11 (0.24), residues: 407 sheet: 0.75 (0.30), residues: 282 loop : 0.14 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.016 0.001 TYR R 92 PHE 0.010 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9022) covalent geometry : angle 0.45966 / 0.25 (12223) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.73716 / 0.42 ( 6) hydrogen bonds : bond 0.04072 / 2.72 ( 477) hydrogen bonds : angle 4.17025 / 2.97 ( 1353) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8186 (tttt) cc_final: 0.7916 (ttpp) REVERT: A 186 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 207 GLU cc_start: 0.7655 (tp30) cc_final: 0.6723 (tt0) REVERT: A 247 MET cc_start: 0.7866 (mtt) cc_final: 0.7521 (mtm) REVERT: A 251 ASP cc_start: 0.8097 (t70) cc_final: 0.7832 (t0) REVERT: A 318 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 330 LYS cc_start: 0.7602 (mttt) cc_final: 0.7330 (mttm) REVERT: A 354 PHE cc_start: 0.8347 (t80) cc_final: 0.7590 (t80) REVERT: B 42 ARG cc_start: 0.8315 (ttt90) cc_final: 0.7919 (ttm-80) REVERT: B 46 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7726 (mtp-110) REVERT: B 138 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: B 170 ASP cc_start: 0.7848 (t70) cc_final: 0.7561 (t70) REVERT: B 198 LEU cc_start: 0.8474 (mt) cc_final: 0.8235 (mt) REVERT: B 219 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7477 (mmm160) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: B 259 GLN cc_start: 0.8674 (pt0) cc_final: 0.8291 (pt0) REVERT: B 262 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8321 (ttm) REVERT: E 160 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.6872 (mtp85) REVERT: E 186 GLN cc_start: 0.8022 (tt0) cc_final: 0.7747 (pt0) REVERT: E 213 THR cc_start: 0.8190 (m) cc_final: 0.7826 (p) REVERT: E 218 ARG cc_start: 0.7335 (mpp-170) cc_final: 0.6948 (mtt90) REVERT: E 223 ASP cc_start: 0.6659 (m-30) cc_final: 0.6368 (m-30) REVERT: E 234 GLU cc_start: 0.8836 (pt0) cc_final: 0.8627 (pt0) REVERT: R 149 SER cc_start: 0.8404 (m) cc_final: 0.8131 (p) REVERT: R 323 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: R 326 MET cc_start: 0.7435 (ttp) cc_final: 0.7157 (ttm) outliers start: 29 outliers final: 14 residues processed: 162 average time/residue: 0.4513 time to fit residues: 78.2250 Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099567 restraints weight = 10477.268| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.23 r_work: 0.2941 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9026 Z= 0.161 Angle : 0.494 7.536 12229 Z= 0.268 Chirality : 0.042 0.141 1403 Planarity : 0.004 0.040 1532 Dihedral : 5.473 52.955 1265 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.17 % Allowed : 12.25 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.95 (0.25), residues: 1118 helix: 3.00 (0.24), residues: 407 sheet: 0.65 (0.30), residues: 281 loop : 0.10 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.017 0.001 TYR R 92 PHE 0.017 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 9022) covalent geometry : angle 0.49396 / 0.27 (12223) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.87409 / 0.50 ( 6) hydrogen bonds : bond 0.04161 / 2.78 ( 477) hydrogen bonds : angle 4.20189 / 3.02 ( 1353) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8195 (tttt) cc_final: 0.7912 (ttpp) REVERT: A 186 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 207 GLU cc_start: 0.7796 (tp30) cc_final: 0.6732 (tt0) REVERT: A 247 MET cc_start: 0.7835 (mtt) cc_final: 0.7498 (mtm) REVERT: A 251 ASP cc_start: 0.8082 (t70) cc_final: 0.7859 (t0) REVERT: A 330 LYS cc_start: 0.7627 (mttt) cc_final: 0.7328 (mttm) REVERT: B 42 ARG cc_start: 0.8361 (ttt90) cc_final: 0.7691 (mmm160) REVERT: B 46 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7786 (mtp-110) REVERT: B 138 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: B 170 ASP cc_start: 0.7953 (t70) cc_final: 0.7651 (t70) REVERT: B 198 LEU cc_start: 0.8464 (mt) cc_final: 0.8242 (mt) REVERT: B 219 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7445 (mmm160) REVERT: B 234 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: B 259 GLN cc_start: 0.8655 (pt0) cc_final: 0.8240 (pt0) REVERT: B 262 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8410 (ttm) REVERT: E 160 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.6841 (mtp85) REVERT: E 186 GLN cc_start: 0.8213 (tt0) cc_final: 0.7902 (tt0) REVERT: E 218 ARG cc_start: 0.7358 (mpp-170) cc_final: 0.6903 (mtt90) REVERT: E 223 ASP cc_start: 0.6887 (m-30) cc_final: 0.6530 (m-30) REVERT: E 234 GLU cc_start: 0.8816 (pt0) cc_final: 0.8604 (pt0) REVERT: R 149 SER cc_start: 0.8390 (m) cc_final: 0.8132 (p) REVERT: R 323 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: R 326 MET cc_start: 0.7433 (ttp) cc_final: 0.7167 (ttm) outliers start: 30 outliers final: 17 residues processed: 159 average time/residue: 0.4409 time to fit residues: 74.9235 Evaluate side-chains 157 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 81 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098843 restraints weight = 10447.850| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.23 r_work: 0.2925 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9026 Z= 0.147 Angle : 0.481 8.088 12229 Z= 0.261 Chirality : 0.042 0.139 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.463 54.412 1265 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.27 % Allowed : 11.83 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.97 (0.25), residues: 1118 helix: 3.05 (0.24), residues: 407 sheet: 0.68 (0.30), residues: 284 loop : 0.07 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.015 0.001 TYR R 92 PHE 0.015 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9022) covalent geometry : angle 0.48123 / 0.26 (12223) SS BOND : bond 0.00332 / 0.17 ( 3) SS BOND : angle 0.75230 / 0.43 ( 6) hydrogen bonds : bond 0.03972 / 2.65 ( 477) hydrogen bonds : angle 4.12627 / 2.96 ( 1353) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.264 Fit side-chains REVERT: A 29 LYS cc_start: 0.8211 (tttt) cc_final: 0.7933 (ttpp) REVERT: A 186 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8360 (mt-10) REVERT: A 207 GLU cc_start: 0.7803 (tp30) cc_final: 0.6993 (tt0) REVERT: A 247 MET cc_start: 0.7854 (mtt) cc_final: 0.7532 (mtm) REVERT: A 251 ASP cc_start: 0.8074 (t70) cc_final: 0.7842 (t0) REVERT: A 330 LYS cc_start: 0.7620 (mttt) cc_final: 0.7303 (mttm) REVERT: B 42 ARG cc_start: 0.8387 (ttt90) cc_final: 0.7762 (mmm160) REVERT: B 46 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7791 (mtp-110) REVERT: B 138 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: B 170 ASP cc_start: 0.7975 (t70) cc_final: 0.7727 (t70) REVERT: B 219 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7503 (mmm160) REVERT: B 234 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: B 259 GLN cc_start: 0.8597 (pt0) cc_final: 0.8160 (pt0) REVERT: B 262 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8355 (ttm) REVERT: E 160 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.6837 (mtp85) REVERT: E 186 GLN cc_start: 0.8205 (tt0) cc_final: 0.7851 (tt0) REVERT: E 223 ASP cc_start: 0.6843 (m-30) cc_final: 0.6509 (m-30) REVERT: E 234 GLU cc_start: 0.8868 (pt0) cc_final: 0.8662 (pt0) REVERT: R 127 CYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7040 (t) REVERT: R 149 SER cc_start: 0.8388 (m) cc_final: 0.8144 (p) REVERT: R 191 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7204 (pt) REVERT: R 323 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: R 326 MET cc_start: 0.7456 (ttp) cc_final: 0.7189 (ttm) outliers start: 31 outliers final: 17 residues processed: 161 average time/residue: 0.4317 time to fit residues: 74.6739 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 179 GLN R 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099193 restraints weight = 10408.673| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.23 r_work: 0.2941 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9026 Z= 0.132 Angle : 0.474 8.526 12229 Z= 0.255 Chirality : 0.041 0.138 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.417 55.890 1265 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.96 % Allowed : 12.78 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.01 (0.25), residues: 1118 helix: 3.12 (0.24), residues: 407 sheet: 0.66 (0.30), residues: 294 loop : 0.06 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.001 TYR R 92 PHE 0.013 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9022) covalent geometry : angle 0.47373 / 0.25 (12223) SS BOND : bond 0.00317 / 0.16 ( 3) SS BOND : angle 0.65962 / 0.37 ( 6) hydrogen bonds : bond 0.03811 / 2.55 ( 477) hydrogen bonds : angle 4.06331 / 2.92 ( 1353) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.344 Fit side-chains REVERT: A 29 LYS cc_start: 0.8147 (tttt) cc_final: 0.7840 (ttpp) REVERT: A 186 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 207 GLU cc_start: 0.7802 (tp30) cc_final: 0.6763 (tt0) REVERT: A 247 MET cc_start: 0.7918 (mtt) cc_final: 0.7614 (mtm) REVERT: A 251 ASP cc_start: 0.8063 (t70) cc_final: 0.7831 (t0) REVERT: A 330 LYS cc_start: 0.7616 (mttt) cc_final: 0.7311 (mttm) REVERT: B 42 ARG cc_start: 0.8408 (ttt90) cc_final: 0.7761 (mmm160) REVERT: B 46 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7829 (mtp-110) REVERT: B 138 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 170 ASP cc_start: 0.7961 (t70) cc_final: 0.7748 (t70) REVERT: B 219 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7582 (mmm160) REVERT: B 234 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 259 GLN cc_start: 0.8608 (pt0) cc_final: 0.8175 (pt0) REVERT: B 262 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8350 (ttm) REVERT: E 160 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.6835 (mtp85) REVERT: E 186 GLN cc_start: 0.8116 (tt0) cc_final: 0.7776 (pt0) REVERT: E 223 ASP cc_start: 0.6878 (m-30) cc_final: 0.6574 (m-30) REVERT: R 127 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7000 (t) REVERT: R 149 SER cc_start: 0.8374 (m) cc_final: 0.8143 (p) REVERT: R 191 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7342 (pp) REVERT: R 323 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: R 326 MET cc_start: 0.7411 (ttp) cc_final: 0.7153 (ttm) outliers start: 28 outliers final: 16 residues processed: 155 average time/residue: 0.4903 time to fit residues: 81.2028 Evaluate side-chains 153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103144 restraints weight = 10438.337| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.23 r_work: 0.2961 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9026 Z= 0.117 Angle : 0.461 8.825 12229 Z= 0.247 Chirality : 0.041 0.136 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.354 57.378 1265 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.96 % Allowed : 12.99 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.05 (0.26), residues: 1118 helix: 3.21 (0.24), residues: 407 sheet: 0.64 (0.30), residues: 294 loop : 0.05 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9022) covalent geometry : angle 0.46090 / 0.25 (12223) SS BOND : bond 0.00274 / 0.14 ( 3) SS BOND : angle 0.61519 / 0.34 ( 6) hydrogen bonds : bond 0.03674 / 2.45 ( 477) hydrogen bonds : angle 3.97714 / 2.86 ( 1353) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.203 Fit side-chains REVERT: A 29 LYS cc_start: 0.8179 (tttt) cc_final: 0.7859 (ttpp) REVERT: A 186 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8352 (mt-10) REVERT: A 207 GLU cc_start: 0.7785 (tp30) cc_final: 0.6739 (tt0) REVERT: A 247 MET cc_start: 0.7881 (mtt) cc_final: 0.7603 (mtm) REVERT: A 251 ASP cc_start: 0.8052 (t70) cc_final: 0.7830 (t0) REVERT: A 330 LYS cc_start: 0.7624 (mttt) cc_final: 0.7323 (mttm) REVERT: B 42 ARG cc_start: 0.8401 (ttt90) cc_final: 0.7755 (mmm160) REVERT: B 46 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7827 (mtp-110) REVERT: B 138 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: B 219 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7551 (mmm160) REVERT: B 234 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 259 GLN cc_start: 0.8663 (pt0) cc_final: 0.8242 (pt0) REVERT: C 47 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7777 (mp0) REVERT: E 93 MET cc_start: 0.8279 (ttp) cc_final: 0.7963 (ttt) REVERT: E 160 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6826 (mtp85) REVERT: E 186 GLN cc_start: 0.8141 (tt0) cc_final: 0.7820 (pt0) REVERT: E 213 THR cc_start: 0.8059 (m) cc_final: 0.7707 (p) REVERT: E 223 ASP cc_start: 0.6781 (m-30) cc_final: 0.6455 (m-30) REVERT: R 127 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7266 (t) REVERT: R 149 SER cc_start: 0.8358 (m) cc_final: 0.8148 (p) REVERT: R 191 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7343 (pp) REVERT: R 323 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: R 326 MET cc_start: 0.7396 (ttp) cc_final: 0.7137 (ttm) outliers start: 28 outliers final: 18 residues processed: 159 average time/residue: 0.4665 time to fit residues: 79.4074 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101954 restraints weight = 10350.875| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.22 r_work: 0.2934 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9026 Z= 0.134 Angle : 0.483 9.044 12229 Z= 0.258 Chirality : 0.041 0.137 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.400 57.895 1265 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.85 % Allowed : 13.83 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.00 (0.25), residues: 1118 helix: 3.18 (0.24), residues: 407 sheet: 0.68 (0.30), residues: 286 loop : -0.04 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.013 0.001 TYR R 92 PHE 0.013 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9022) covalent geometry : angle 0.48305 / 0.26 (12223) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 0.63748 / 0.35 ( 6) hydrogen bonds : bond 0.03776 / 2.52 ( 477) hydrogen bonds : angle 3.98875 / 2.87 ( 1353) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.353 Fit side-chains REVERT: A 29 LYS cc_start: 0.8189 (tttt) cc_final: 0.7863 (ttpp) REVERT: A 53 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5728 (mmt) REVERT: A 186 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 207 GLU cc_start: 0.7792 (tp30) cc_final: 0.6747 (tt0) REVERT: A 247 MET cc_start: 0.7904 (mtt) cc_final: 0.7612 (mtm) REVERT: A 251 ASP cc_start: 0.8039 (t70) cc_final: 0.7823 (t0) REVERT: A 330 LYS cc_start: 0.7607 (mttt) cc_final: 0.7315 (mttm) REVERT: B 42 ARG cc_start: 0.8392 (ttt90) cc_final: 0.7748 (mmm160) REVERT: B 46 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7832 (mtp-110) REVERT: B 138 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: B 219 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7526 (mmm160) REVERT: B 234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: B 259 GLN cc_start: 0.8610 (pt0) cc_final: 0.8171 (pt0) REVERT: C 47 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7756 (mp0) REVERT: E 160 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6817 (mtp85) REVERT: E 186 GLN cc_start: 0.8155 (tt0) cc_final: 0.7835 (tt0) REVERT: E 223 ASP cc_start: 0.6807 (m-30) cc_final: 0.6478 (m-30) REVERT: R 127 CYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7232 (t) REVERT: R 149 SER cc_start: 0.8365 (m) cc_final: 0.8163 (p) REVERT: R 180 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6034 (mpp) REVERT: R 191 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7278 (pp) REVERT: R 323 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: R 326 MET cc_start: 0.7610 (ttp) cc_final: 0.7373 (ttm) outliers start: 27 outliers final: 18 residues processed: 153 average time/residue: 0.5187 time to fit residues: 84.7677 Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100281 restraints weight = 10402.707| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.21 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9026 Z= 0.124 Angle : 0.475 9.162 12229 Z= 0.254 Chirality : 0.041 0.136 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.377 59.351 1265 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.96 % Allowed : 13.83 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.04 (0.25), residues: 1118 helix: 3.24 (0.24), residues: 407 sheet: 0.63 (0.30), residues: 288 loop : -0.00 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9022) covalent geometry : angle 0.47447 / 0.25 (12223) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.62809 / 0.34 ( 6) hydrogen bonds : bond 0.03670 / 2.46 ( 477) hydrogen bonds : angle 3.94724 / 2.84 ( 1353) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.340 Fit side-chains REVERT: A 29 LYS cc_start: 0.8244 (tttt) cc_final: 0.7939 (ttpp) REVERT: A 53 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5741 (mmt) REVERT: A 186 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 207 GLU cc_start: 0.7815 (tp30) cc_final: 0.6767 (tt0) REVERT: A 247 MET cc_start: 0.7879 (mtt) cc_final: 0.7585 (mtm) REVERT: A 251 ASP cc_start: 0.8035 (t70) cc_final: 0.7831 (t0) REVERT: A 330 LYS cc_start: 0.7595 (mttt) cc_final: 0.7309 (mttm) REVERT: B 42 ARG cc_start: 0.8387 (ttt90) cc_final: 0.7752 (mmm160) REVERT: B 46 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7813 (mtp-110) REVERT: B 138 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: B 219 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7532 (mmm160) REVERT: B 234 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 259 GLN cc_start: 0.8650 (pt0) cc_final: 0.8221 (pt0) REVERT: C 47 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7730 (mp0) REVERT: E 93 MET cc_start: 0.8272 (ttp) cc_final: 0.7953 (ttt) REVERT: E 160 ARG cc_start: 0.7461 (mtp-110) cc_final: 0.6804 (mtp85) REVERT: E 186 GLN cc_start: 0.8121 (tt0) cc_final: 0.7827 (tt0) REVERT: E 213 THR cc_start: 0.8078 (m) cc_final: 0.7707 (p) REVERT: E 223 ASP cc_start: 0.6806 (m-30) cc_final: 0.6468 (m-30) REVERT: R 149 SER cc_start: 0.8364 (m) cc_final: 0.8163 (p) REVERT: R 180 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6018 (mpp) REVERT: R 191 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7277 (pp) REVERT: R 323 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: R 326 MET cc_start: 0.7607 (ttp) cc_final: 0.7382 (ttm) outliers start: 28 outliers final: 19 residues processed: 155 average time/residue: 0.5370 time to fit residues: 89.1130 Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN R 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099405 restraints weight = 10399.137| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.20 r_work: 0.2915 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9026 Z= 0.161 Angle : 0.509 9.329 12229 Z= 0.272 Chirality : 0.042 0.138 1403 Planarity : 0.004 0.040 1532 Dihedral : 5.519 58.674 1265 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.75 % Allowed : 14.36 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.89 (0.25), residues: 1118 helix: 3.06 (0.24), residues: 408 sheet: 0.63 (0.29), residues: 286 loop : -0.08 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.014 0.001 TYR R 92 PHE 0.016 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9022) covalent geometry : angle 0.50897 / 0.27 (12223) SS BOND : bond 0.00284 / 0.14 ( 3) SS BOND : angle 1.04762 / 0.60 ( 6) hydrogen bonds : bond 0.03945 / 2.63 ( 477) hydrogen bonds : angle 4.06345 / 2.93 ( 1353) Misc. bond : bond 0.00046 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.339 Fit side-chains REVERT: A 29 LYS cc_start: 0.8202 (tttt) cc_final: 0.7893 (ttpp) REVERT: A 53 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5830 (mmt) REVERT: A 186 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 216 GLU cc_start: 0.8965 (tt0) cc_final: 0.8735 (tt0) REVERT: A 247 MET cc_start: 0.7909 (mtt) cc_final: 0.7641 (mtm) REVERT: A 251 ASP cc_start: 0.8044 (t70) cc_final: 0.7843 (t0) REVERT: A 330 LYS cc_start: 0.7593 (mttt) cc_final: 0.7308 (mttm) REVERT: B 42 ARG cc_start: 0.8422 (ttt90) cc_final: 0.7754 (mmm160) REVERT: B 46 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7783 (mtp-110) REVERT: B 138 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: B 219 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7496 (mmm160) REVERT: B 234 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: C 47 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7760 (mp0) REVERT: E 160 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6816 (mtp85) REVERT: E 186 GLN cc_start: 0.8136 (tt0) cc_final: 0.7810 (tt0) REVERT: R 180 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6025 (mpp) REVERT: R 323 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: R 326 MET cc_start: 0.7620 (ttp) cc_final: 0.7395 (ttm) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.5573 time to fit residues: 86.8321 Evaluate side-chains 149 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100354 restraints weight = 10285.366| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.21 r_work: 0.2941 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9026 Z= 0.120 Angle : 0.481 9.416 12229 Z= 0.257 Chirality : 0.041 0.135 1403 Planarity : 0.003 0.040 1532 Dihedral : 5.415 59.563 1265 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.53 % Allowed : 14.78 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.99 (0.25), residues: 1118 helix: 3.20 (0.24), residues: 408 sheet: 0.59 (0.30), residues: 288 loop : -0.02 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9022) covalent geometry : angle 0.48086 / 0.26 (12223) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.89669 / 0.51 ( 6) hydrogen bonds : bond 0.03645 / 2.43 ( 477) hydrogen bonds : angle 3.96415 / 2.86 ( 1353) Misc. bond : bond 0.00029 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.89 seconds wall clock time: 53 minutes 25.56 seconds (3205.56 seconds total)