Starting phenix.real_space_refine on Fri Aug 22 22:42:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9o_39865/08_2025/8z9o_39865.cif" } resolution = 2.4 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5270 2.51 5 N 1443 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8279 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2558 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1829 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2448 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain: "R" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 2.38, per 1000 atoms: 0.29 Number of scatterers: 8279 At special positions: 0 Unit cell: (75.33, 101.37, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1514 8.00 N 1443 7.00 C 5270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - 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=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 433.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 42.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.657A pdb=" N GLU C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.583A pdb=" N GLN C 236 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.636A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.768A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.955A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 18 through 47 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 69 removed outlier: 3.766A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 79 removed outlier: 3.767A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 121 removed outlier: 3.612A pdb=" N TYR R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE R 105 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.519A pdb=" N CYS R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 259 through 289 removed outlier: 5.469A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU R 277 " --> pdb=" O ALA R 273 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 310 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.499A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.891A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.821A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.758A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.816A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.325A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.663A pdb=" N PHE C 219 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 224 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N ALA C 243 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ALA C 249 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.283A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 158 through 160 432 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2217 1.33 - 1.45: 1656 1.45 - 1.57: 4521 1.57 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8464 Sorted by residual: bond pdb=" C PRO R 20 " pdb=" N PRO R 21 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.30e-02 5.92e+03 4.86e+01 bond pdb=" CA TRP R 73 " pdb=" C TRP R 73 " ideal model delta sigma weight residual 1.519 1.468 0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" N TRP R 73 " pdb=" CA TRP R 73 " ideal model delta sigma weight residual 1.458 1.403 0.054 1.35e-02 5.49e+03 1.60e+01 bond pdb=" CG HIS R 79 " pdb=" ND1 HIS R 79 " ideal model delta sigma weight residual 1.378 1.335 0.043 1.10e-02 8.26e+03 1.54e+01 bond pdb=" CG HIS R 85 " pdb=" ND1 HIS R 85 " ideal model delta sigma weight residual 1.378 1.335 0.043 1.10e-02 8.26e+03 1.50e+01 ... (remaining 8459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 11256 2.48 - 4.96: 196 4.96 - 7.45: 26 7.45 - 9.93: 7 9.93 - 12.41: 1 Bond angle restraints: 11486 Sorted by residual: angle pdb=" N TRP R 73 " pdb=" CA TRP R 73 " pdb=" C TRP R 73 " ideal model delta sigma weight residual 113.43 101.02 12.41 1.26e+00 6.30e-01 9.70e+01 angle pdb=" CA HIS R 10 " pdb=" CB HIS R 10 " pdb=" CG HIS R 10 " ideal model delta sigma weight residual 113.80 106.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" C PRO R 20 " pdb=" N PRO R 21 " pdb=" CA PRO R 21 " ideal model delta sigma weight residual 118.97 124.57 -5.60 1.04e+00 9.25e-01 2.90e+01 angle pdb=" CA HIS R 80 " pdb=" CB HIS R 80 " pdb=" CG HIS R 80 " ideal model delta sigma weight residual 113.80 109.12 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" CA HIS R 79 " pdb=" CB HIS R 79 " pdb=" CG HIS R 79 " ideal model delta sigma weight residual 113.80 109.19 4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4680 17.93 - 35.85: 366 35.85 - 53.78: 49 53.78 - 71.71: 15 71.71 - 89.63: 7 Dihedral angle restraints: 5117 sinusoidal: 2080 harmonic: 3037 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 0.00 -28.46 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CB CYS R 9 " pdb=" SG CYS R 9 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -45.99 -40.01 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE R 307 " pdb=" C PHE R 307 " pdb=" N LEU R 308 " pdb=" CA LEU R 308 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1220 0.105 - 0.210: 55 0.210 - 0.314: 2 0.314 - 0.419: 2 0.419 - 0.524: 2 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C10 CLR R 401 " pdb=" C1 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C9 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1278 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " 0.043 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO R 21 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 188 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C VAL R 188 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL R 188 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY R 189 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 285 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C LEU R 285 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU R 285 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR R 286 " 0.015 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 925 2.74 - 3.28: 8148 3.28 - 3.82: 14102 3.82 - 4.36: 17285 4.36 - 4.90: 29353 Nonbonded interactions: 69813 Sorted by model distance: nonbonded pdb=" O LEU R 146 " pdb=" OG SER R 150 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.251 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.275 3.120 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.290 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.298 3.040 ... (remaining 69808 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 8468 Z= 0.340 Angle : 0.818 12.408 11494 Z= 0.504 Chirality : 0.055 0.524 1281 Planarity : 0.005 0.066 1463 Dihedral : 13.392 89.632 3141 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.23), residues: 1026 helix: -0.82 (0.22), residues: 396 sheet: -0.35 (0.34), residues: 219 loop : -1.94 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 38 TYR 0.018 0.002 TYR R 76 PHE 0.024 0.002 PHE R 159 TRP 0.015 0.002 TRP R 73 HIS 0.015 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 8464) covalent geometry : angle 0.81774 (11486) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.32677 ( 8) hydrogen bonds : bond 0.16402 ( 432) hydrogen bonds : angle 6.91238 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6883 (ttm-80) REVERT: B 45 MET cc_start: 0.8628 (mtt) cc_final: 0.8123 (mtm) REVERT: B 219 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7358 (mmt180) REVERT: C 35 GLN cc_start: 0.8086 (mt0) cc_final: 0.7843 (mm-40) REVERT: C 339 TYR cc_start: 0.8429 (m-80) cc_final: 0.8026 (m-80) REVERT: C 392 GLU cc_start: 0.7423 (mp0) cc_final: 0.7122 (mp0) REVERT: G 38 MET cc_start: 0.8050 (ttp) cc_final: 0.7833 (ttp) REVERT: R 57 MET cc_start: 0.7559 (ttt) cc_final: 0.7313 (tpp) REVERT: R 263 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.6960 (mtp85) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.5236 time to fit residues: 114.8171 Evaluate side-chains 134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN B 239 ASN B 266 HIS C 14 ASN C 41 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN R 45 GLN R 100 ASN R 164 ASN R 217 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125462 restraints weight = 8539.759| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.82 r_work: 0.3319 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8468 Z= 0.147 Angle : 0.587 7.457 11494 Z= 0.317 Chirality : 0.044 0.177 1281 Planarity : 0.005 0.059 1463 Dihedral : 5.654 55.447 1276 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.09 % Allowed : 10.77 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.25), residues: 1026 helix: 0.98 (0.26), residues: 397 sheet: -0.05 (0.33), residues: 224 loop : -1.11 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 44 TYR 0.013 0.002 TYR R 102 PHE 0.030 0.002 PHE R 307 TRP 0.020 0.002 TRP B 82 HIS 0.010 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8464) covalent geometry : angle 0.58583 (11486) SS BOND : bond 0.00110 ( 4) SS BOND : angle 1.40615 ( 8) hydrogen bonds : bond 0.04901 ( 432) hydrogen bonds : angle 5.02741 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8395 (mt0) cc_final: 0.8182 (mp10) REVERT: B 45 MET cc_start: 0.8926 (mtt) cc_final: 0.8379 (mtm) REVERT: B 59 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8239 (t80) REVERT: B 134 ARG cc_start: 0.7603 (mmp-170) cc_final: 0.6785 (mmm160) REVERT: B 217 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8325 (pmt) REVERT: C 20 ARG cc_start: 0.6676 (mtm110) cc_final: 0.6299 (mtt90) REVERT: C 24 LYS cc_start: 0.7832 (mttm) cc_final: 0.6971 (ttpt) REVERT: C 25 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8084 (mtpt) REVERT: C 35 GLN cc_start: 0.8302 (mt0) cc_final: 0.7877 (mm-40) REVERT: C 339 TYR cc_start: 0.8609 (m-80) cc_final: 0.8290 (m-80) REVERT: C 385 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.6972 (tmt170) REVERT: N 5 GLN cc_start: 0.8137 (mt0) cc_final: 0.7537 (mm-40) REVERT: N 120 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: R 14 ARG cc_start: 0.7192 (mmt90) cc_final: 0.6767 (ptp90) REVERT: R 57 MET cc_start: 0.7916 (ttt) cc_final: 0.7663 (tpp) REVERT: R 263 ARG cc_start: 0.7103 (mtp-110) cc_final: 0.6579 (mtp85) outliers start: 27 outliers final: 11 residues processed: 156 average time/residue: 0.5212 time to fit residues: 85.8278 Evaluate side-chains 149 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.0170 chunk 48 optimal weight: 0.0000 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 44 GLN B 75 GLN B 176 GLN B 220 GLN C 294 GLN C 357 HIS R 165 HIS R 269 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.179029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120069 restraints weight = 8043.532| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.92 r_work: 0.3208 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8468 Z= 0.101 Angle : 0.501 7.127 11494 Z= 0.268 Chirality : 0.041 0.171 1281 Planarity : 0.004 0.061 1463 Dihedral : 5.053 43.690 1276 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.86 % Allowed : 13.29 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1026 helix: 1.71 (0.26), residues: 396 sheet: 0.22 (0.34), residues: 221 loop : -0.92 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 44 TYR 0.013 0.001 TYR R 98 PHE 0.027 0.001 PHE R 307 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8464) covalent geometry : angle 0.50067 (11486) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.90490 ( 8) hydrogen bonds : bond 0.03892 ( 432) hydrogen bonds : angle 4.57217 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8893 (mtt) cc_final: 0.8283 (mtm) REVERT: B 59 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 134 ARG cc_start: 0.7583 (mmp-170) cc_final: 0.7159 (mmp-170) REVERT: B 172 GLU cc_start: 0.7920 (tp30) cc_final: 0.7678 (mm-30) REVERT: B 217 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8417 (pmt) REVERT: C 20 ARG cc_start: 0.6458 (mtm110) cc_final: 0.5992 (mtt90) REVERT: C 24 LYS cc_start: 0.7702 (mttm) cc_final: 0.6740 (ttpt) REVERT: C 34 LYS cc_start: 0.8658 (tttm) cc_final: 0.8382 (tttp) REVERT: C 35 GLN cc_start: 0.8103 (mt0) cc_final: 0.7597 (mm-40) REVERT: C 339 TYR cc_start: 0.8297 (m-80) cc_final: 0.7979 (m-80) REVERT: G 38 MET cc_start: 0.8196 (ttp) cc_final: 0.7544 (mtm) REVERT: G 42 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: N 5 GLN cc_start: 0.8124 (mt0) cc_final: 0.7413 (mm-40) REVERT: R 263 ARG cc_start: 0.7037 (mtp-110) cc_final: 0.6515 (mtp85) outliers start: 25 outliers final: 7 residues processed: 154 average time/residue: 0.5026 time to fit residues: 81.7379 Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 96 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN N 35 ASN R 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116678 restraints weight = 8101.749| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.95 r_work: 0.3159 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8468 Z= 0.111 Angle : 0.509 6.954 11494 Z= 0.274 Chirality : 0.042 0.166 1281 Planarity : 0.004 0.055 1463 Dihedral : 5.014 37.307 1276 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.09 % Allowed : 15.01 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1026 helix: 1.97 (0.26), residues: 397 sheet: 0.33 (0.34), residues: 222 loop : -0.71 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 44 TYR 0.011 0.001 TYR R 102 PHE 0.026 0.002 PHE R 307 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8464) covalent geometry : angle 0.50893 (11486) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.97220 ( 8) hydrogen bonds : bond 0.04094 ( 432) hydrogen bonds : angle 4.51718 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: B 45 MET cc_start: 0.8846 (mtt) cc_final: 0.8298 (mtm) REVERT: B 134 ARG cc_start: 0.7621 (mmp-170) cc_final: 0.7197 (mmp-170) REVERT: B 197 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7751 (mmm160) REVERT: B 217 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8439 (pmt) REVERT: C 20 ARG cc_start: 0.6656 (mtm110) cc_final: 0.6219 (mtt90) REVERT: C 24 LYS cc_start: 0.7722 (mttm) cc_final: 0.6773 (ttpt) REVERT: C 34 LYS cc_start: 0.8643 (tttm) cc_final: 0.8375 (tttp) REVERT: C 35 GLN cc_start: 0.8145 (mt0) cc_final: 0.7625 (mm-40) REVERT: C 339 TYR cc_start: 0.8335 (m-80) cc_final: 0.8058 (m-80) REVERT: N 5 GLN cc_start: 0.8124 (mt0) cc_final: 0.7392 (mm-40) REVERT: R 155 HIS cc_start: 0.8061 (m-70) cc_final: 0.7857 (m-70) REVERT: R 234 LEU cc_start: 0.7434 (tp) cc_final: 0.7215 (tp) REVERT: R 263 ARG cc_start: 0.7082 (mtp-110) cc_final: 0.6558 (mtp85) outliers start: 27 outliers final: 10 residues processed: 159 average time/residue: 0.4867 time to fit residues: 81.7618 Evaluate side-chains 149 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 92 optimal weight: 0.0770 chunk 68 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 35 ASN R 47 GLN R 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.178904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119463 restraints weight = 8087.435| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.95 r_work: 0.3201 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8468 Z= 0.097 Angle : 0.484 6.841 11494 Z= 0.259 Chirality : 0.041 0.178 1281 Planarity : 0.004 0.054 1463 Dihedral : 4.802 34.334 1276 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.63 % Allowed : 15.69 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.27), residues: 1026 helix: 2.12 (0.26), residues: 398 sheet: 0.44 (0.35), residues: 211 loop : -0.67 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 14 TYR 0.010 0.001 TYR R 102 PHE 0.024 0.001 PHE R 307 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8464) covalent geometry : angle 0.48380 (11486) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.70980 ( 8) hydrogen bonds : bond 0.03693 ( 432) hydrogen bonds : angle 4.36900 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: B 134 ARG cc_start: 0.7554 (mmp-170) cc_final: 0.6760 (mmm160) REVERT: C 20 ARG cc_start: 0.6589 (mtm110) cc_final: 0.6164 (mtt90) REVERT: C 24 LYS cc_start: 0.7696 (mttm) cc_final: 0.6745 (ttpt) REVERT: C 34 LYS cc_start: 0.8638 (tttm) cc_final: 0.8381 (tttp) REVERT: C 35 GLN cc_start: 0.8094 (mt0) cc_final: 0.7595 (mm-40) REVERT: C 339 TYR cc_start: 0.8309 (m-80) cc_final: 0.8037 (m-80) REVERT: N 5 GLN cc_start: 0.8127 (mt0) cc_final: 0.7434 (OUTLIER) REVERT: R 155 HIS cc_start: 0.8037 (m-70) cc_final: 0.7835 (m-70) REVERT: R 263 ARG cc_start: 0.7160 (mtp-110) cc_final: 0.6645 (mtp85) outliers start: 23 outliers final: 11 residues processed: 155 average time/residue: 0.5049 time to fit residues: 82.6187 Evaluate side-chains 146 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN N 35 ASN R 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112894 restraints weight = 7897.903| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.96 r_work: 0.3107 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8468 Z= 0.150 Angle : 0.555 6.689 11494 Z= 0.298 Chirality : 0.043 0.191 1281 Planarity : 0.004 0.052 1463 Dihedral : 5.069 35.005 1276 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.21 % Allowed : 15.92 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.27), residues: 1026 helix: 2.04 (0.26), residues: 402 sheet: 0.45 (0.35), residues: 212 loop : -0.60 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.012 0.002 TYR R 201 PHE 0.023 0.002 PHE N 108 TRP 0.016 0.002 TRP B 82 HIS 0.010 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8464) covalent geometry : angle 0.55426 (11486) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.99821 ( 8) hydrogen bonds : bond 0.04541 ( 432) hydrogen bonds : angle 4.64221 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.222 Fit side-chains REVERT: B 44 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: B 134 ARG cc_start: 0.7620 (mmp-170) cc_final: 0.6823 (mmm160) REVERT: B 172 GLU cc_start: 0.7965 (tp30) cc_final: 0.7729 (mm-30) REVERT: C 20 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6213 (mtt90) REVERT: C 24 LYS cc_start: 0.7699 (mttm) cc_final: 0.6808 (ttpt) REVERT: C 35 GLN cc_start: 0.8195 (mt0) cc_final: 0.7665 (mm-40) REVERT: C 314 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: C 339 TYR cc_start: 0.8378 (m-80) cc_final: 0.8025 (m-80) REVERT: N 5 GLN cc_start: 0.8076 (mt0) cc_final: 0.7343 (OUTLIER) REVERT: N 65 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8303 (ttpt) REVERT: R 155 HIS cc_start: 0.8120 (m-70) cc_final: 0.7881 (m-70) REVERT: R 263 ARG cc_start: 0.7276 (mtp-110) cc_final: 0.6711 (mtp85) REVERT: R 269 HIS cc_start: 0.7275 (m-70) cc_final: 0.6994 (m90) outliers start: 28 outliers final: 14 residues processed: 149 average time/residue: 0.4783 time to fit residues: 75.4417 Evaluate side-chains 144 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112204 restraints weight = 7945.460| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.95 r_work: 0.3095 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8468 Z= 0.158 Angle : 0.568 6.575 11494 Z= 0.306 Chirality : 0.044 0.204 1281 Planarity : 0.004 0.051 1463 Dihedral : 5.160 36.559 1276 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.09 % Allowed : 16.72 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.27), residues: 1026 helix: 2.00 (0.26), residues: 398 sheet: 0.45 (0.35), residues: 214 loop : -0.46 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.012 0.002 TYR R 201 PHE 0.026 0.002 PHE N 108 TRP 0.016 0.002 TRP B 82 HIS 0.011 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8464) covalent geometry : angle 0.56685 (11486) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.49775 ( 8) hydrogen bonds : bond 0.04661 ( 432) hydrogen bonds : angle 4.66371 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.317 Fit side-chains REVERT: B 134 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.6937 (mmm160) REVERT: B 172 GLU cc_start: 0.7987 (tp30) cc_final: 0.7765 (mm-30) REVERT: C 20 ARG cc_start: 0.6666 (mtm110) cc_final: 0.6236 (mtt90) REVERT: C 24 LYS cc_start: 0.7698 (mttm) cc_final: 0.6815 (ttpt) REVERT: C 35 GLN cc_start: 0.8232 (mt0) cc_final: 0.7693 (mm-40) REVERT: C 339 TYR cc_start: 0.8379 (m-80) cc_final: 0.8001 (m-80) REVERT: N 5 GLN cc_start: 0.8101 (mt0) cc_final: 0.7341 (mm-40) REVERT: N 65 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8273 (ttpt) REVERT: R 155 HIS cc_start: 0.8082 (m-70) cc_final: 0.7775 (m-70) REVERT: R 263 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.6730 (mtp85) REVERT: R 269 HIS cc_start: 0.7241 (m-70) cc_final: 0.7001 (m90) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 0.5022 time to fit residues: 76.4647 Evaluate side-chains 144 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116929 restraints weight = 7932.365| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.95 r_work: 0.3163 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8468 Z= 0.106 Angle : 0.510 6.538 11494 Z= 0.274 Chirality : 0.041 0.190 1281 Planarity : 0.004 0.051 1463 Dihedral : 4.771 36.400 1276 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.95 % Allowed : 17.87 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.27), residues: 1026 helix: 2.18 (0.27), residues: 397 sheet: 0.52 (0.35), residues: 217 loop : -0.45 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 44 TYR 0.010 0.001 TYR R 102 PHE 0.020 0.001 PHE R 307 TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8464) covalent geometry : angle 0.50971 (11486) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.16453 ( 8) hydrogen bonds : bond 0.03864 ( 432) hydrogen bonds : angle 4.40165 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.191 Fit side-chains REVERT: B 44 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: B 134 ARG cc_start: 0.7608 (mmp-170) cc_final: 0.7166 (mmt180) REVERT: B 197 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.7827 (mtp85) REVERT: C 20 ARG cc_start: 0.6638 (mtm110) cc_final: 0.6175 (mtt90) REVERT: C 24 LYS cc_start: 0.7697 (mttm) cc_final: 0.6763 (ttpt) REVERT: C 34 LYS cc_start: 0.8636 (tttm) cc_final: 0.8341 (tttp) REVERT: C 35 GLN cc_start: 0.8103 (mt0) cc_final: 0.7578 (mm-40) REVERT: C 339 TYR cc_start: 0.8359 (m-80) cc_final: 0.8023 (m-80) REVERT: N 5 GLN cc_start: 0.8140 (mt0) cc_final: 0.7388 (mm-40) REVERT: N 73 ASP cc_start: 0.8413 (t0) cc_final: 0.8013 (t0) REVERT: R 14 ARG cc_start: 0.6715 (mtm-85) cc_final: 0.5580 (pmm150) REVERT: R 79 HIS cc_start: 0.7217 (m-70) cc_final: 0.7011 (m170) REVERT: R 155 HIS cc_start: 0.8107 (m-70) cc_final: 0.7829 (m-70) REVERT: R 269 HIS cc_start: 0.7169 (m-70) cc_final: 0.6965 (m90) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.4864 time to fit residues: 75.0671 Evaluate side-chains 146 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN C 213 GLN C 292 ASN N 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110276 restraints weight = 7899.383| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.94 r_work: 0.3064 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8468 Z= 0.198 Angle : 0.616 7.553 11494 Z= 0.334 Chirality : 0.045 0.208 1281 Planarity : 0.005 0.050 1463 Dihedral : 5.300 39.626 1276 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.75 % Allowed : 17.41 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.26), residues: 1026 helix: 1.92 (0.26), residues: 399 sheet: 0.44 (0.35), residues: 213 loop : -0.45 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 44 TYR 0.018 0.002 TYR R 201 PHE 0.026 0.002 PHE N 108 TRP 0.015 0.002 TRP B 82 HIS 0.014 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8464) covalent geometry : angle 0.61349 (11486) SS BOND : bond 0.00198 ( 4) SS BOND : angle 2.19122 ( 8) hydrogen bonds : bond 0.05169 ( 432) hydrogen bonds : angle 4.81810 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.213 Fit side-chains REVERT: B 44 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: B 134 ARG cc_start: 0.7757 (mmp-170) cc_final: 0.7087 (mmm160) REVERT: C 20 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6354 (mtt90) REVERT: C 24 LYS cc_start: 0.7715 (mttm) cc_final: 0.6843 (ttpt) REVERT: C 35 GLN cc_start: 0.8235 (mt0) cc_final: 0.7691 (mm-40) REVERT: C 339 TYR cc_start: 0.8439 (m-80) cc_final: 0.8012 (m-80) REVERT: N 5 GLN cc_start: 0.8101 (mt0) cc_final: 0.7375 (mm-40) REVERT: R 79 HIS cc_start: 0.7424 (m-70) cc_final: 0.7215 (m-70) REVERT: R 127 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6450 (ptt90) REVERT: R 155 HIS cc_start: 0.8151 (m-70) cc_final: 0.7828 (m-70) REVERT: R 263 ARG cc_start: 0.7256 (mtp-110) cc_final: 0.6681 (mtp85) REVERT: R 269 HIS cc_start: 0.7305 (m-70) cc_final: 0.7092 (m90) outliers start: 24 outliers final: 14 residues processed: 145 average time/residue: 0.5070 time to fit residues: 77.4995 Evaluate side-chains 143 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113019 restraints weight = 7950.040| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.95 r_work: 0.3109 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8468 Z= 0.137 Angle : 0.551 5.870 11494 Z= 0.297 Chirality : 0.043 0.205 1281 Planarity : 0.004 0.050 1463 Dihedral : 5.048 37.710 1276 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.06 % Allowed : 17.98 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.27), residues: 1026 helix: 2.00 (0.26), residues: 399 sheet: 0.51 (0.35), residues: 217 loop : -0.49 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 44 TYR 0.012 0.001 TYR B 59 PHE 0.022 0.002 PHE N 108 TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8464) covalent geometry : angle 0.54903 (11486) SS BOND : bond 0.00193 ( 4) SS BOND : angle 1.73806 ( 8) hydrogen bonds : bond 0.04441 ( 432) hydrogen bonds : angle 4.64787 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.293 Fit side-chains REVERT: B 134 ARG cc_start: 0.7715 (mmp-170) cc_final: 0.7254 (mmt180) REVERT: B 197 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7805 (mmm160) REVERT: C 20 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6311 (mtt90) REVERT: C 24 LYS cc_start: 0.7720 (mttm) cc_final: 0.6783 (ttpt) REVERT: C 34 LYS cc_start: 0.8668 (tttm) cc_final: 0.8384 (tttp) REVERT: C 35 GLN cc_start: 0.8191 (mt0) cc_final: 0.7656 (mm-40) REVERT: C 339 TYR cc_start: 0.8381 (m-80) cc_final: 0.8013 (m-80) REVERT: N 5 GLN cc_start: 0.8077 (mt0) cc_final: 0.7346 (mm-40) REVERT: N 73 ASP cc_start: 0.8459 (t0) cc_final: 0.8063 (t0) REVERT: R 14 ARG cc_start: 0.6768 (mtm-85) cc_final: 0.5683 (pmm150) REVERT: R 79 HIS cc_start: 0.7360 (m-70) cc_final: 0.7134 (m-70) REVERT: R 127 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6414 (ptt90) REVERT: R 155 HIS cc_start: 0.8155 (m-70) cc_final: 0.7849 (m-70) REVERT: R 269 HIS cc_start: 0.7194 (m-70) cc_final: 0.6988 (m90) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.5079 time to fit residues: 72.4043 Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111623 restraints weight = 7920.795| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.94 r_work: 0.3087 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8468 Z= 0.158 Angle : 0.574 6.518 11494 Z= 0.310 Chirality : 0.044 0.213 1281 Planarity : 0.004 0.050 1463 Dihedral : 5.148 37.897 1276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.29 % Allowed : 17.87 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1026 helix: 1.97 (0.26), residues: 398 sheet: 0.61 (0.34), residues: 207 loop : -0.53 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 44 TYR 0.013 0.002 TYR R 76 PHE 0.023 0.002 PHE N 108 TRP 0.017 0.002 TRP B 82 HIS 0.012 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8464) covalent geometry : angle 0.57202 (11486) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.85145 ( 8) hydrogen bonds : bond 0.04722 ( 432) hydrogen bonds : angle 4.72137 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.00 seconds wall clock time: 58 minutes 44.29 seconds (3524.29 seconds total)