Starting phenix.real_space_refine on Thu Jul 2 10:39:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.map" model { file = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izb_35838/07_2026/8izb_35838.cif" } resolution = 3.06 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= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 59 5.16 5 C 5315 2.51 5 N 1416 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 8322 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1954 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2246 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {'CLR': 2, 'UBL': 1} Inner-chain residues flagged as termini: ['pdbres="SER R 502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.16 Number of scatterers: 8322 At special positions: 0 Unit cell: (79.18, 102.72, 133.75, 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 59 16.00 P 1 15.00 O 1531 8.00 N 1416 7.00 C 5315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 168 " 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: 0.64 Conformation dependent library (CDL) restraints added in 395.7 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 43.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.520A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.083A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.610A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.646A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 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: 3.527A 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 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 16 through 52 removed outlier: 3.989A pdb=" N VAL R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 55 through 71 Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.574A pdb=" N TYR R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 79 " --> pdb=" O ARG R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 122 removed outlier: 3.569A pdb=" N PHE R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS R 98 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 126 removed outlier: 3.660A pdb=" N PHE R 126 " --> pdb=" O PRO R 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 123 through 126' Processing helix chain 'R' and resid 128 through 132 Processing helix chain 'R' and resid 134 through 149 Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 168 through 172 Processing helix chain 'R' and resid 178 through 194 Processing helix chain 'R' and resid 194 through 212 Processing helix chain 'R' and resid 223 through 258 Proline residue: R 245 - end of helix Proline residue: R 251 - end of helix removed outlier: 3.608A pdb=" N LEU R 255 " --> pdb=" O PRO R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 283 removed outlier: 3.679A pdb=" N ARG R 268 " --> pdb=" O CYS R 264 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 293 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 304 removed outlier: 3.595A pdb=" N ARG R 300 " --> pdb=" O THR R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.250A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.797A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.698A 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: 6.745A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.961A 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: 6.184A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.308A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.696A 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: 4.485A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.272A 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: 6.570A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.960A 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: 3.949A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.850A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1340 1.31 - 1.43: 2360 1.43 - 1.56: 4716 1.56 - 1.68: 5 1.68 - 1.81: 82 Bond restraints: 8503 Sorted by residual: bond pdb=" CAK UBL R 501 " pdb=" OAJ UBL R 501 " ideal model delta sigma weight residual 1.326 1.413 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" OAF UBL R 501 " pdb=" PAC UBL R 501 " ideal model delta sigma weight residual 1.727 1.659 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CAR UBL R 501 " pdb=" CAS UBL R 501 " ideal model delta sigma weight residual 1.497 1.556 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" CAT UBL R 501 " pdb=" CAU UBL R 501 " ideal model delta sigma weight residual 1.498 1.550 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" CAX UBL R 501 " pdb=" CAY UBL R 501 " ideal model delta sigma weight residual 1.524 1.565 -0.041 2.00e-02 2.50e+03 4.10e+00 ... (remaining 8498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 11521 5.02 - 10.04: 10 10.04 - 15.06: 0 15.06 - 20.08: 1 20.08 - 25.10: 1 Bond angle restraints: 11533 Sorted by residual: angle pdb=" CAR UBL R 501 " pdb=" CAS UBL R 501 " pdb=" CAT UBL R 501 " ideal model delta sigma weight residual 127.71 152.81 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CAS UBL R 501 " pdb=" CAT UBL R 501 " pdb=" CAU UBL R 501 " ideal model delta sigma weight residual 127.34 112.18 15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" OAA UBL R 501 " pdb=" PAC UBL R 501 " pdb=" OAF UBL R 501 " ideal model delta sigma weight residual 100.39 109.65 -9.26 3.00e+00 1.11e-01 9.54e+00 angle pdb=" CAL UBL R 501 " pdb=" CAK UBL R 501 " pdb=" OAJ UBL R 501 " ideal model delta sigma weight residual 111.99 120.58 -8.59 3.00e+00 1.11e-01 8.20e+00 angle pdb=" C13 CLR R 504 " pdb=" C17 CLR R 504 " pdb=" C20 CLR R 504 " ideal model delta sigma weight residual 119.60 111.25 8.35 3.00e+00 1.11e-01 7.74e+00 ... (remaining 11528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 4769 14.17 - 28.35: 212 28.35 - 42.52: 47 42.52 - 56.69: 19 56.69 - 70.86: 1 Dihedral angle restraints: 5048 sinusoidal: 1992 harmonic: 3056 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1234 0.095 - 0.189: 60 0.189 - 0.284: 1 0.284 - 0.378: 3 0.378 - 0.473: 2 Chirality restraints: 1300 Sorted by residual: chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C10 CLR R 503 " pdb=" C1 CLR R 503 " pdb=" C5 CLR R 503 " pdb=" C9 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.85 -2.51 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1297 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 288 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO R 289 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO R 289 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 289 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.48e-01 pdb=" N PRO C 55 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.014 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1421 2.77 - 3.30: 7890 3.30 - 3.83: 13826 3.83 - 4.37: 17165 4.37 - 4.90: 29479 Nonbonded interactions: 69781 Sorted by model distance: nonbonded pdb=" OG SER A 205 " pdb=" O ASP B 118 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.262 3.040 nonbonded pdb=" O CYS R 204 " pdb=" OG1 THR R 208 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP A 381 " pdb=" NH1 ARG A 385 " model vdw 2.285 3.120 nonbonded pdb=" O LEU R 97 " pdb=" ND2 ASN R 101 " model vdw 2.300 3.120 ... (remaining 69776 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: 0.440 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.105 8507 Z= 0.175 Angle : 0.535 25.103 11539 Z= 0.231 Chirality : 0.047 0.473 1300 Planarity : 0.003 0.042 1457 Dihedral : 9.070 70.863 3065 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.68 % Allowed : 4.17 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1031 helix: 1.14 (0.26), residues: 387 sheet: 0.68 (0.32), residues: 230 loop : 0.18 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.007 0.001 TYR N 60 PHE 0.013 0.001 PHE R 119 TRP 0.012 0.001 TRP A 234 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 8503) covalent geometry : angle 0.53492 / 0.23 (11533) SS BOND : bond 0.00146 / 0.07 ( 3) SS BOND : angle 0.65081 / 0.38 ( 6) hydrogen bonds : bond 0.25651 / 16.73 ( 429) hydrogen bonds : angle 7.90595 / 5.45 ( 1197) Misc. bond : bond 0.10502 / 5.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 245 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 20 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7524 (ttp-110) REVERT: A 34 LYS cc_start: 0.8475 (tttt) cc_final: 0.8259 (tttp) REVERT: A 35 GLN cc_start: 0.7932 (tp40) cc_final: 0.7439 (mm-40) REVERT: A 53 LYS cc_start: 0.8725 (pttp) cc_final: 0.8330 (pttt) REVERT: A 211 LYS cc_start: 0.8532 (mtmt) cc_final: 0.7973 (mttp) REVERT: A 221 MET cc_start: 0.8789 (ttp) cc_final: 0.8558 (ttp) REVERT: A 307 LYS cc_start: 0.9009 (mttt) cc_final: 0.8569 (mtmm) REVERT: A 358 TYR cc_start: 0.8896 (m-80) cc_final: 0.8495 (m-80) REVERT: A 381 ASP cc_start: 0.8918 (t70) cc_final: 0.8651 (t0) REVERT: B 101 MET cc_start: 0.8493 (mtp) cc_final: 0.8275 (mtp) REVERT: B 217 MET cc_start: 0.6948 (ppp) cc_final: 0.5926 (ppp) REVERT: B 219 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7350 (mmp80) REVERT: B 254 ASP cc_start: 0.8289 (t70) cc_final: 0.7893 (t0) REVERT: C 38 MET cc_start: 0.8554 (ttp) cc_final: 0.8306 (ttm) REVERT: N 70 ILE cc_start: 0.8776 (tt) cc_final: 0.8336 (tt) REVERT: N 73 ASP cc_start: 0.7293 (t0) cc_final: 0.6955 (t0) REVERT: N 108 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: N 120 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8178 (mm-40) REVERT: R 21 ILE cc_start: 0.8703 (mt) cc_final: 0.8480 (mt) REVERT: R 113 SER cc_start: 0.9003 (t) cc_final: 0.8766 (m) REVERT: R 147 LEU cc_start: 0.8235 (tp) cc_final: 0.7846 (mp) REVERT: R 227 LYS cc_start: 0.7785 (mttt) cc_final: 0.7464 (tttt) REVERT: R 250 PHE cc_start: 0.8574 (t80) cc_final: 0.8358 (t80) REVERT: R 294 PHE cc_start: 0.8633 (m-80) cc_final: 0.8341 (m-10) outliers start: 6 outliers final: 2 residues processed: 250 average time/residue: 0.0910 time to fit residues: 29.4633 Evaluate side-chains 169 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 19 GLN A 213 GLN B 6 GLN B 91 HIS B 220 GLN B 259 GLN N 3 GLN N 31 ASN N 82 GLN R 226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114884 restraints weight = 9820.893| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.37 r_work: 0.2952 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 8507 Z= 0.315 Angle : 0.674 7.779 11539 Z= 0.358 Chirality : 0.048 0.176 1300 Planarity : 0.005 0.049 1457 Dihedral : 6.447 59.813 1197 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.27 % Allowed : 9.24 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1031 helix: 1.72 (0.26), residues: 394 sheet: 0.10 (0.31), residues: 229 loop : 0.14 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 333 TYR 0.018 0.002 TYR R 47 PHE 0.039 0.003 PHE R 119 TRP 0.015 0.003 TRP B 169 HIS 0.005 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.32 ( 8503) covalent geometry : angle 0.67233 / 0.36 (11533) SS BOND : bond 0.00431 / 0.21 ( 3) SS BOND : angle 1.87265 / 1.07 ( 6) hydrogen bonds : bond 0.05969 / 3.90 ( 429) hydrogen bonds : angle 5.42695 / 3.77 ( 1197) Misc. bond : bond 0.00172 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7367 (ttp-110) REVERT: A 35 GLN cc_start: 0.7963 (tp40) cc_final: 0.7172 (tt0) REVERT: A 211 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8171 (mttp) REVERT: A 213 GLN cc_start: 0.8621 (tt0) cc_final: 0.8374 (tt0) REVERT: A 307 LYS cc_start: 0.9082 (mttt) cc_final: 0.8610 (mtmm) REVERT: A 335 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 101 MET cc_start: 0.8951 (mtp) cc_final: 0.8561 (mtt) REVERT: B 137 ARG cc_start: 0.8166 (mmp80) cc_final: 0.7923 (mmp80) REVERT: B 196 THR cc_start: 0.8737 (m) cc_final: 0.8403 (p) REVERT: B 219 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7418 (mmp80) REVERT: B 254 ASP cc_start: 0.8739 (t70) cc_final: 0.8250 (t0) REVERT: B 280 LYS cc_start: 0.9146 (tttm) cc_final: 0.8945 (tttp) REVERT: C 20 LYS cc_start: 0.8411 (mttt) cc_final: 0.7918 (mtmm) REVERT: N 70 ILE cc_start: 0.8754 (tt) cc_final: 0.8478 (tt) REVERT: N 73 ASP cc_start: 0.7471 (t0) cc_final: 0.7174 (t0) REVERT: N 77 ASN cc_start: 0.8209 (m-40) cc_final: 0.7965 (t0) REVERT: N 120 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8340 (mm-40) REVERT: R 22 TYR cc_start: 0.8388 (m-10) cc_final: 0.8112 (m-10) REVERT: R 45 TYR cc_start: 0.7429 (t80) cc_final: 0.7200 (t80) REVERT: R 127 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.6998 (m90) REVERT: R 172 LEU cc_start: 0.8448 (mt) cc_final: 0.7917 (mp) REVERT: R 183 VAL cc_start: 0.8840 (t) cc_final: 0.8611 (p) outliers start: 29 outliers final: 20 residues processed: 197 average time/residue: 0.0861 time to fit residues: 22.1183 Evaluate side-chains 176 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 279 ASN R 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119462 restraints weight = 9719.565| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.32 r_work: 0.3037 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8507 Z= 0.126 Angle : 0.511 5.998 11539 Z= 0.269 Chirality : 0.042 0.148 1300 Planarity : 0.004 0.045 1457 Dihedral : 6.042 59.919 1197 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.82 % Allowed : 11.05 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1031 helix: 2.17 (0.26), residues: 394 sheet: 0.06 (0.32), residues: 226 loop : 0.17 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.015 0.001 TYR N 60 PHE 0.027 0.002 PHE R 119 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8503) covalent geometry : angle 0.51092 / 0.27 (11533) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 0.94672 / 0.53 ( 6) hydrogen bonds : bond 0.04263 / 2.80 ( 429) hydrogen bonds : angle 4.82818 / 3.36 ( 1197) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 35 GLN cc_start: 0.7857 (tp40) cc_final: 0.7074 (tt0) REVERT: A 211 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8150 (mttp) REVERT: A 213 GLN cc_start: 0.8461 (tt0) cc_final: 0.8080 (tt0) REVERT: A 307 LYS cc_start: 0.9054 (mttt) cc_final: 0.8585 (mtmm) REVERT: A 358 TYR cc_start: 0.9079 (m-80) cc_final: 0.8629 (m-80) REVERT: B 137 ARG cc_start: 0.8080 (mmp80) cc_final: 0.7766 (mmp80) REVERT: B 196 THR cc_start: 0.8731 (m) cc_final: 0.8417 (p) REVERT: B 219 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7344 (mmp80) REVERT: B 226 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8573 (mt-10) REVERT: B 254 ASP cc_start: 0.8698 (t70) cc_final: 0.8230 (t0) REVERT: B 259 GLN cc_start: 0.8145 (pt0) cc_final: 0.7834 (pt0) REVERT: N 70 ILE cc_start: 0.8861 (tt) cc_final: 0.8577 (tt) REVERT: N 73 ASP cc_start: 0.7504 (t0) cc_final: 0.7211 (t0) REVERT: N 76 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8479 (mtpp) REVERT: N 108 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: N 120 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8285 (mm-40) REVERT: R 92 MET cc_start: 0.8686 (mmp) cc_final: 0.8476 (mmm) REVERT: R 127 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6832 (m90) REVERT: R 183 VAL cc_start: 0.8765 (t) cc_final: 0.8551 (p) outliers start: 25 outliers final: 14 residues processed: 188 average time/residue: 0.1062 time to fit residues: 26.0768 Evaluate side-chains 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN B 32 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119549 restraints weight = 9871.356| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.37 r_work: 0.3046 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8507 Z= 0.121 Angle : 0.496 6.705 11539 Z= 0.261 Chirality : 0.041 0.152 1300 Planarity : 0.003 0.043 1457 Dihedral : 5.662 58.668 1195 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.82 % Allowed : 13.19 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1031 helix: 2.33 (0.26), residues: 394 sheet: 0.20 (0.33), residues: 218 loop : 0.11 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 18 TYR 0.014 0.001 TYR N 60 PHE 0.026 0.001 PHE R 119 TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8503) covalent geometry : angle 0.49584 / 0.26 (11533) SS BOND : bond 0.00122 / 0.06 ( 3) SS BOND : angle 0.75226 / 0.44 ( 6) hydrogen bonds : bond 0.03943 / 2.58 ( 429) hydrogen bonds : angle 4.63627 / 3.22 ( 1197) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7477 (t0) REVERT: A 35 GLN cc_start: 0.7934 (tp40) cc_final: 0.7194 (tt0) REVERT: A 211 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8193 (mttp) REVERT: A 213 GLN cc_start: 0.8401 (tt0) cc_final: 0.8038 (tt0) REVERT: A 307 LYS cc_start: 0.8996 (mttt) cc_final: 0.8631 (mtmm) REVERT: A 358 TYR cc_start: 0.9042 (m-80) cc_final: 0.8653 (m-80) REVERT: B 17 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 137 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7879 (mmp80) REVERT: B 219 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7353 (mmp80) REVERT: B 245 SER cc_start: 0.8984 (m) cc_final: 0.8779 (p) REVERT: B 254 ASP cc_start: 0.8718 (t70) cc_final: 0.8298 (t0) REVERT: B 259 GLN cc_start: 0.8235 (pt0) cc_final: 0.7904 (pt0) REVERT: N 70 ILE cc_start: 0.8815 (tt) cc_final: 0.8511 (tt) REVERT: N 73 ASP cc_start: 0.7553 (t0) cc_final: 0.7250 (t0) REVERT: N 76 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8750 (mmmm) REVERT: N 108 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: N 120 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8261 (mm-40) REVERT: R 127 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6850 (m90) REVERT: R 191 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7029 (tt) outliers start: 25 outliers final: 18 residues processed: 183 average time/residue: 0.0998 time to fit residues: 23.9731 Evaluate side-chains 183 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 98 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121671 restraints weight = 9824.014| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.36 r_work: 0.3075 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8507 Z= 0.102 Angle : 0.480 6.409 11539 Z= 0.252 Chirality : 0.040 0.151 1300 Planarity : 0.003 0.040 1457 Dihedral : 5.488 59.252 1195 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.04 % Allowed : 13.08 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1031 helix: 2.44 (0.26), residues: 396 sheet: 0.18 (0.33), residues: 220 loop : 0.12 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.013 0.001 TYR N 60 PHE 0.026 0.001 PHE R 119 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8503) covalent geometry : angle 0.47993 / 0.25 (11533) SS BOND : bond 0.00120 / 0.06 ( 3) SS BOND : angle 0.56819 / 0.32 ( 6) hydrogen bonds : bond 0.03664 / 2.40 ( 429) hydrogen bonds : angle 4.49336 / 3.12 ( 1197) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7287 (mtm110) REVERT: A 23 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7733 (t0) REVERT: A 211 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8221 (mttp) REVERT: A 213 GLN cc_start: 0.8318 (tt0) cc_final: 0.7943 (tt0) REVERT: A 307 LYS cc_start: 0.8999 (mttt) cc_final: 0.8556 (mtmm) REVERT: A 333 ARG cc_start: 0.8800 (mtm180) cc_final: 0.8575 (mtm180) REVERT: A 358 TYR cc_start: 0.9013 (m-80) cc_final: 0.8599 (m-80) REVERT: B 17 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 137 ARG cc_start: 0.8066 (mmp80) cc_final: 0.7852 (mmp80) REVERT: B 196 THR cc_start: 0.8654 (m) cc_final: 0.8145 (p) REVERT: B 214 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8014 (mtt-85) REVERT: B 219 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7318 (mmp80) REVERT: B 254 ASP cc_start: 0.8692 (t70) cc_final: 0.8291 (t0) REVERT: N 70 ILE cc_start: 0.8806 (tt) cc_final: 0.8513 (tt) REVERT: N 73 ASP cc_start: 0.7556 (t0) cc_final: 0.7253 (t0) REVERT: N 76 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8713 (mmmm) REVERT: N 108 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: N 120 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8204 (mm-40) REVERT: R 127 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6738 (m90) REVERT: R 191 LEU cc_start: 0.7511 (tp) cc_final: 0.7131 (tt) outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 0.0932 time to fit residues: 23.0533 Evaluate side-chains 181 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122048 restraints weight = 9721.483| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.30 r_work: 0.3161 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8507 Z= 0.106 Angle : 0.485 7.344 11539 Z= 0.251 Chirality : 0.040 0.152 1300 Planarity : 0.003 0.042 1457 Dihedral : 5.182 58.273 1193 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.83 % Allowed : 12.85 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1031 helix: 2.47 (0.26), residues: 396 sheet: 0.22 (0.33), residues: 220 loop : 0.12 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 18 TYR 0.013 0.001 TYR N 60 PHE 0.026 0.001 PHE R 119 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS R 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8503) covalent geometry : angle 0.48446 / 0.25 (11533) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 0.56368 / 0.31 ( 6) hydrogen bonds : bond 0.03577 / 2.33 ( 429) hydrogen bonds : angle 4.42059 / 3.07 ( 1197) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7480 (mtm110) REVERT: A 211 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8311 (mttp) REVERT: A 213 GLN cc_start: 0.8294 (tt0) cc_final: 0.7955 (tt0) REVERT: A 307 LYS cc_start: 0.8953 (mttt) cc_final: 0.8623 (mtmm) REVERT: A 338 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8417 (ttmt) REVERT: A 358 TYR cc_start: 0.8981 (m-80) cc_final: 0.8629 (m-80) REVERT: B 17 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 196 THR cc_start: 0.8745 (m) cc_final: 0.8287 (p) REVERT: B 219 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7468 (mmp80) REVERT: B 254 ASP cc_start: 0.8695 (t70) cc_final: 0.8380 (t0) REVERT: N 70 ILE cc_start: 0.8785 (tt) cc_final: 0.8479 (tt) REVERT: N 73 ASP cc_start: 0.7615 (t0) cc_final: 0.7296 (t0) REVERT: N 76 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8647 (mmmm) REVERT: N 108 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: N 120 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8179 (mm-40) REVERT: R 191 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7260 (tt) outliers start: 34 outliers final: 22 residues processed: 180 average time/residue: 0.1043 time to fit residues: 24.6781 Evaluate side-chains 179 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 40 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 220 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120396 restraints weight = 9822.383| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.33 r_work: 0.3074 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8507 Z= 0.108 Angle : 0.476 6.579 11539 Z= 0.248 Chirality : 0.041 0.157 1300 Planarity : 0.003 0.039 1457 Dihedral : 5.119 57.549 1193 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.06 % Allowed : 12.06 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.27), residues: 1031 helix: 2.52 (0.26), residues: 396 sheet: 0.26 (0.33), residues: 225 loop : 0.19 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.014 0.001 TYR N 60 PHE 0.027 0.001 PHE R 119 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8503) covalent geometry : angle 0.47558 / 0.25 (11533) SS BOND : bond 0.00118 / 0.06 ( 3) SS BOND : angle 0.67091 / 0.38 ( 6) hydrogen bonds : bond 0.03508 / 2.29 ( 429) hydrogen bonds : angle 4.37675 / 3.04 ( 1197) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7326 (mtm110) REVERT: A 23 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7230 (t0) REVERT: A 211 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8187 (mttp) REVERT: A 213 GLN cc_start: 0.8305 (tt0) cc_final: 0.7907 (tt0) REVERT: A 307 LYS cc_start: 0.8921 (mttt) cc_final: 0.8545 (mtmm) REVERT: A 338 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8276 (ttmt) REVERT: A 358 TYR cc_start: 0.9007 (m-80) cc_final: 0.8648 (m-80) REVERT: B 17 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 146 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8778 (tt) REVERT: B 219 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7294 (mmp80) REVERT: B 254 ASP cc_start: 0.8662 (t70) cc_final: 0.8215 (t0) REVERT: N 70 ILE cc_start: 0.8782 (tt) cc_final: 0.8460 (tt) REVERT: N 73 ASP cc_start: 0.7593 (t0) cc_final: 0.7258 (t0) REVERT: N 76 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8655 (mmmm) REVERT: N 108 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: R 191 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7145 (tt) outliers start: 36 outliers final: 21 residues processed: 184 average time/residue: 0.0980 time to fit residues: 23.6440 Evaluate side-chains 182 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116396 restraints weight = 9931.777| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.34 r_work: 0.3103 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8507 Z= 0.180 Angle : 0.543 7.184 11539 Z= 0.283 Chirality : 0.043 0.154 1300 Planarity : 0.004 0.040 1457 Dihedral : 5.292 57.139 1193 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.49 % Allowed : 13.30 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1031 helix: 2.43 (0.26), residues: 395 sheet: 0.11 (0.33), residues: 227 loop : 0.17 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.014 0.001 TYR N 60 PHE 0.032 0.002 PHE R 119 TRP 0.013 0.002 TRP A 281 HIS 0.003 0.001 HIS R 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 8503) covalent geometry : angle 0.54223 / 0.28 (11533) SS BOND : bond 0.00234 / 0.11 ( 3) SS BOND : angle 1.03574 / 0.61 ( 6) hydrogen bonds : bond 0.04046 / 2.61 ( 429) hydrogen bonds : angle 4.54929 / 3.16 ( 1197) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7453 (mtm-85) REVERT: A 35 GLN cc_start: 0.7999 (tp40) cc_final: 0.7357 (tt0) REVERT: A 211 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8270 (mttp) REVERT: A 213 GLN cc_start: 0.8450 (tt0) cc_final: 0.8209 (tt0) REVERT: A 307 LYS cc_start: 0.8953 (mttt) cc_final: 0.8634 (mtmm) REVERT: A 338 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8642 (ttmt) REVERT: A 358 TYR cc_start: 0.9012 (m-80) cc_final: 0.8686 (m-80) REVERT: B 17 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 219 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7427 (mmp80) REVERT: B 254 ASP cc_start: 0.8793 (t70) cc_final: 0.8414 (t0) REVERT: N 70 ILE cc_start: 0.8775 (tt) cc_final: 0.8431 (tt) REVERT: N 73 ASP cc_start: 0.7702 (t0) cc_final: 0.7366 (t0) REVERT: N 76 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8637 (mmmm) REVERT: R 92 MET cc_start: 0.8559 (mmm) cc_final: 0.8240 (mmm) REVERT: R 127 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6550 (m170) REVERT: R 172 LEU cc_start: 0.8522 (mt) cc_final: 0.8076 (mp) REVERT: R 191 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7217 (tt) REVERT: R 273 PHE cc_start: 0.8765 (t80) cc_final: 0.8521 (t80) outliers start: 31 outliers final: 25 residues processed: 173 average time/residue: 0.0909 time to fit residues: 20.5183 Evaluate side-chains 181 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120067 restraints weight = 9778.802| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.32 r_work: 0.3089 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8507 Z= 0.127 Angle : 0.510 8.568 11539 Z= 0.264 Chirality : 0.041 0.166 1300 Planarity : 0.003 0.038 1457 Dihedral : 5.218 56.606 1193 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.27 % Allowed : 13.75 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1031 helix: 2.44 (0.26), residues: 396 sheet: 0.16 (0.33), residues: 225 loop : 0.21 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.016 0.001 TYR N 60 PHE 0.028 0.001 PHE R 119 TRP 0.015 0.002 TRP B 82 HIS 0.002 0.001 HIS R 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8503) covalent geometry : angle 0.51012 / 0.26 (11533) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.77745 / 0.46 ( 6) hydrogen bonds : bond 0.03705 / 2.41 ( 429) hydrogen bonds : angle 4.46818 / 3.10 ( 1197) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7337 (mtm-85) REVERT: A 35 GLN cc_start: 0.7915 (tp40) cc_final: 0.7238 (tt0) REVERT: A 211 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8196 (mttp) REVERT: A 213 GLN cc_start: 0.8375 (tt0) cc_final: 0.8156 (tt0) REVERT: A 307 LYS cc_start: 0.8937 (mttt) cc_final: 0.8541 (mtmm) REVERT: A 358 TYR cc_start: 0.8991 (m-80) cc_final: 0.8646 (m-80) REVERT: B 17 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 212 ASP cc_start: 0.8384 (t0) cc_final: 0.8022 (t0) REVERT: B 219 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7332 (mmp80) REVERT: B 254 ASP cc_start: 0.8707 (t70) cc_final: 0.8302 (t0) REVERT: N 70 ILE cc_start: 0.8774 (tt) cc_final: 0.8449 (tt) REVERT: N 73 ASP cc_start: 0.7668 (t0) cc_final: 0.7302 (t0) REVERT: N 76 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8652 (mmmm) REVERT: R 92 MET cc_start: 0.8576 (mmm) cc_final: 0.8228 (mmm) REVERT: R 127 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6472 (m170) REVERT: R 172 LEU cc_start: 0.8490 (mt) cc_final: 0.7999 (mp) REVERT: R 191 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7165 (tt) REVERT: R 273 PHE cc_start: 0.8613 (t80) cc_final: 0.8390 (t80) outliers start: 29 outliers final: 23 residues processed: 174 average time/residue: 0.1032 time to fit residues: 23.4380 Evaluate side-chains 179 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 99 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 61 optimal weight: 0.0000 chunk 75 optimal weight: 0.5980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 29 GLN B 32 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125611 restraints weight = 9823.491| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.30 r_work: 0.3161 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8507 Z= 0.094 Angle : 0.480 8.422 11539 Z= 0.246 Chirality : 0.040 0.176 1300 Planarity : 0.003 0.038 1457 Dihedral : 5.044 55.219 1193 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 14.88 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.27), residues: 1031 helix: 2.66 (0.26), residues: 390 sheet: 0.26 (0.33), residues: 225 loop : 0.29 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.015 0.001 TYR N 60 PHE 0.024 0.001 PHE R 119 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS R 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 8503) covalent geometry : angle 0.47947 / 0.25 (11533) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.55891 / 0.33 ( 6) hydrogen bonds : bond 0.03336 / 2.19 ( 429) hydrogen bonds : angle 4.30927 / 2.98 ( 1197) Misc. bond : bond 0.00013 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7254 (mtm-85) REVERT: A 23 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7255 (t0) REVERT: A 211 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8250 (mttp) REVERT: A 213 GLN cc_start: 0.8288 (tt0) cc_final: 0.7985 (tt0) REVERT: A 307 LYS cc_start: 0.8922 (mttt) cc_final: 0.8563 (mtmm) REVERT: A 358 TYR cc_start: 0.8931 (m-80) cc_final: 0.8614 (m-80) REVERT: B 17 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 32 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: B 212 ASP cc_start: 0.8200 (t0) cc_final: 0.7857 (t0) REVERT: B 219 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7325 (mmp80) REVERT: B 254 ASP cc_start: 0.8572 (t70) cc_final: 0.8190 (t0) REVERT: C 38 MET cc_start: 0.8375 (ttm) cc_final: 0.7873 (mtp) REVERT: N 70 ILE cc_start: 0.8799 (tt) cc_final: 0.8463 (tt) REVERT: N 73 ASP cc_start: 0.7652 (t0) cc_final: 0.7355 (t0) REVERT: N 76 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8630 (mmmm) REVERT: N 108 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: R 41 LEU cc_start: 0.8773 (mt) cc_final: 0.8325 (mt) REVERT: R 127 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6532 (m170) REVERT: R 191 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7297 (tt) REVERT: R 301 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7432 (mtm-85) outliers start: 21 outliers final: 15 residues processed: 171 average time/residue: 0.1060 time to fit residues: 23.6945 Evaluate side-chains 170 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122421 restraints weight = 9726.925| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.30 r_work: 0.3138 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8507 Z= 0.112 Angle : 0.493 7.771 11539 Z= 0.256 Chirality : 0.041 0.236 1300 Planarity : 0.004 0.055 1457 Dihedral : 5.038 54.870 1193 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 15.90 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1031 helix: 2.45 (0.26), residues: 396 sheet: 0.26 (0.33), residues: 226 loop : 0.25 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.014 0.001 TYR N 60 PHE 0.029 0.001 PHE R 273 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8503) covalent geometry : angle 0.49303 / 0.26 (11533) SS BOND : bond 0.00112 / 0.05 ( 3) SS BOND : angle 0.68223 / 0.40 ( 6) hydrogen bonds : bond 0.03457 / 2.27 ( 429) hydrogen bonds : angle 4.31607 / 2.99 ( 1197) Misc. bond : bond 0.00024 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.01 seconds wall clock time: 37 minutes 56.45 seconds (2276.45 seconds total)