Starting phenix.real_space_refine on Fri Aug 22 20:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8y_37361/08_2025/8w8y_37361.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 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 Ca 1 9.91 5 S 63 5.16 5 C 4875 2.51 5 N 1320 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 7642 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2061 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain breaks: 1 Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 107 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.20, per 1000 atoms: 0.16 Number of scatterers: 7642 At special positions: 0 Unit cell: (76.5, 96.9, 130.05, 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) Ca 1 19.99 S 63 16.00 O 1383 8.00 N 1320 7.00 C 4875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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: 0.36 Conformation dependent library (CDL) restraints added in 265.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 39.9% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'R' and resid 43 through 65 removed outlier: 4.151A pdb=" N GLY R 49 " --> pdb=" O PHE R 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 101 removed outlier: 3.828A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 148 removed outlier: 4.124A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.541A pdb=" N CYS R 175 " --> pdb=" O CYS R 171 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 223 removed outlier: 3.692A pdb=" N CYS R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS R 217 " --> pdb=" O PHE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 265 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 275 through 279 Processing helix chain 'R' and resid 280 through 285 removed outlier: 3.558A pdb=" N LEU R 285 " --> pdb=" O PHE R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 293 Processing helix chain 'R' and resid 294 through 300 removed outlier: 3.508A pdb=" N ALA R 300 " --> pdb=" O PRO R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 310 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.751A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.539A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.681A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.514A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.930A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.770A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.835A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.505A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.578A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.902A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.537A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.596A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.906A 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: 6.804A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.543A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.853A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.525A 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: 3.808A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.096A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1062 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: 0.77 Time building geometry restraints manager: 0.49 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: 1223 1.31 - 1.44: 2173 1.44 - 1.57: 4308 1.57 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 7795 Sorted by residual: bond pdb=" CA GLU A 209 " pdb=" CB GLU A 209 " ideal model delta sigma weight residual 1.534 1.476 0.058 1.60e-02 3.91e+03 1.32e+01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.459 1.415 0.044 1.27e-02 6.20e+03 1.21e+01 bond pdb=" CA GLU A 209 " pdb=" C GLU A 209 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.24e-02 6.50e+03 1.04e+01 bond pdb=" C THR A 210 " pdb=" O THR A 210 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.24e-02 6.50e+03 8.61e+00 bond pdb=" CA THR A 210 " pdb=" C THR A 210 " ideal model delta sigma weight residual 1.519 1.487 0.033 1.14e-02 7.69e+03 8.22e+00 ... (remaining 7790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 10070 1.30 - 2.59: 405 2.59 - 3.89: 68 3.89 - 5.18: 13 5.18 - 6.48: 7 Bond angle restraints: 10563 Sorted by residual: angle pdb=" N ASP L 9 " pdb=" CA ASP L 9 " pdb=" C ASP L 9 " ideal model delta sigma weight residual 113.18 106.97 6.21 1.21e+00 6.83e-01 2.64e+01 angle pdb=" O PHE R 213 " pdb=" C PHE R 213 " pdb=" N ALA R 214 " ideal model delta sigma weight residual 122.12 117.94 4.18 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N ARG R 215 " pdb=" CA ARG R 215 " pdb=" C ARG R 215 " ideal model delta sigma weight residual 111.28 114.96 -3.68 1.09e+00 8.42e-01 1.14e+01 angle pdb=" C GLU A 209 " pdb=" CA GLU A 209 " pdb=" CB GLU A 209 " ideal model delta sigma weight residual 110.24 104.00 6.24 1.88e+00 2.83e-01 1.10e+01 angle pdb=" CA PHE R 213 " pdb=" C PHE R 213 " pdb=" N ALA R 214 " ideal model delta sigma weight residual 117.30 121.12 -3.82 1.16e+00 7.43e-01 1.08e+01 ... (remaining 10558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3970 17.89 - 35.77: 496 35.77 - 53.66: 119 53.66 - 71.55: 19 71.55 - 89.43: 9 Dihedral angle restraints: 4613 sinusoidal: 1767 harmonic: 2846 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -125.69 39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA TYR R 148 " pdb=" C TYR R 148 " pdb=" N ALA R 149 " pdb=" CA ALA R 149 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE R 275 " pdb=" C ILE R 275 " pdb=" N CYS R 276 " pdb=" CA CYS R 276 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 4610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 980 0.054 - 0.109: 204 0.109 - 0.163: 27 0.163 - 0.218: 2 0.218 - 0.272: 1 Chirality restraints: 1214 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PHE A 208 " pdb=" N PHE A 208 " pdb=" C PHE A 208 " pdb=" CB PHE A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1211 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.059 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO G 53 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 236 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO N 88 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.024 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 34 2.52 - 3.11: 5299 3.11 - 3.71: 10915 3.71 - 4.30: 16023 4.30 - 4.90: 28356 Nonbonded interactions: 60627 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 1.922 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 1.995 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 501 " model vdw 2.332 2.510 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.332 3.040 ... (remaining 60622 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: 2.080 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.005 0.058 7797 Z= 0.255 Angle : 0.630 6.480 10567 Z= 0.372 Chirality : 0.045 0.272 1214 Planarity : 0.005 0.088 1334 Dihedral : 16.709 89.433 2761 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.71 % Allowed : 22.74 % Favored : 75.55 % 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 aren not related in a simple way. whole: -0.10 (0.27), residues: 955 helix: 1.17 (0.29), residues: 364 sheet: -0.19 (0.34), residues: 231 loop : -1.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.016 0.002 TYR R 277 PHE 0.013 0.002 PHE B 241 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 7795) covalent geometry : angle 0.62707 (10563) SS BOND : bond 0.00896 ( 2) SS BOND : angle 3.13382 ( 4) hydrogen bonds : bond 0.18498 ( 370) hydrogen bonds : angle 6.37462 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.200 Fit side-chains REVERT: R 264 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6779 (mp) REVERT: B 217 MET cc_start: 0.7984 (ptp) cc_final: 0.7347 (pmt) outliers start: 14 outliers final: 12 residues processed: 141 average time/residue: 0.4500 time to fit residues: 66.9194 Evaluate side-chains 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110539 restraints weight = 8658.331| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7797 Z= 0.165 Angle : 0.552 7.437 10567 Z= 0.298 Chirality : 0.044 0.141 1214 Planarity : 0.004 0.063 1334 Dihedral : 5.708 50.378 1078 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.50 % Allowed : 20.54 % Favored : 73.96 % 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 aren not related in a simple way. whole: 0.19 (0.27), residues: 955 helix: 1.50 (0.29), residues: 365 sheet: 0.09 (0.34), residues: 216 loop : -1.22 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.016 0.001 TYR R 148 PHE 0.014 0.001 PHE B 241 TRP 0.014 0.002 TRP N 47 HIS 0.014 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7795) covalent geometry : angle 0.55137 (10563) SS BOND : bond 0.00481 ( 2) SS BOND : angle 1.31620 ( 4) hydrogen bonds : bond 0.05514 ( 370) hydrogen bonds : angle 4.54176 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.201 Fit side-chains REVERT: R 184 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: R 187 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7042 (tpp) REVERT: B 59 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: B 215 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 356 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7593 (mtm180) outliers start: 45 outliers final: 20 residues processed: 152 average time/residue: 0.4289 time to fit residues: 69.1175 Evaluate side-chains 137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 5 HIS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN N 3 GLN A 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113034 restraints weight = 8590.499| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.11 r_work: 0.3150 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7797 Z= 0.100 Angle : 0.464 6.268 10567 Z= 0.254 Chirality : 0.041 0.137 1214 Planarity : 0.004 0.054 1334 Dihedral : 4.082 18.952 1058 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.65 % Allowed : 21.64 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.27), residues: 955 helix: 1.92 (0.28), residues: 363 sheet: 0.31 (0.34), residues: 216 loop : -1.18 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.013 0.001 TYR N 80 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7795) covalent geometry : angle 0.46343 (10563) SS BOND : bond 0.00504 ( 2) SS BOND : angle 0.82976 ( 4) hydrogen bonds : bond 0.04171 ( 370) hydrogen bonds : angle 4.09479 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.192 Fit side-chains REVERT: R 187 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6615 (tpp) REVERT: R 199 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6895 (mpt) REVERT: R 264 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 59 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: N 80 TYR cc_start: 0.8872 (m-80) cc_final: 0.8272 (m-80) REVERT: A 220 HIS cc_start: 0.8607 (t-170) cc_final: 0.8254 (t70) outliers start: 38 outliers final: 16 residues processed: 144 average time/residue: 0.4220 time to fit residues: 64.2968 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 5 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113446 restraints weight = 8667.649| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.13 r_work: 0.3112 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7797 Z= 0.100 Angle : 0.460 6.006 10567 Z= 0.251 Chirality : 0.041 0.143 1214 Planarity : 0.003 0.050 1334 Dihedral : 3.918 16.707 1057 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.77 % Allowed : 22.25 % Favored : 72.98 % 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 aren not related in a simple way. whole: 0.70 (0.27), residues: 955 helix: 2.03 (0.28), residues: 365 sheet: 0.37 (0.34), residues: 218 loop : -1.07 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 10 TYR 0.011 0.001 TYR R 277 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7795) covalent geometry : angle 0.46016 (10563) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.94610 ( 4) hydrogen bonds : bond 0.03964 ( 370) hydrogen bonds : angle 3.96904 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.287 Fit side-chains REVERT: R 57 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6112 (tp) REVERT: R 199 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6971 (mpt) REVERT: R 264 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6632 (mp) REVERT: L 3 MET cc_start: 0.6690 (ttt) cc_final: 0.6490 (ttm) REVERT: B 59 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: B 212 ASP cc_start: 0.8066 (t0) cc_final: 0.7862 (t0) REVERT: N 80 TYR cc_start: 0.8830 (m-80) cc_final: 0.8250 (m-80) REVERT: A 27 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 314 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7868 (mp0) outliers start: 39 outliers final: 18 residues processed: 138 average time/residue: 0.4400 time to fit residues: 64.3075 Evaluate side-chains 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113732 restraints weight = 8581.434| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.11 r_work: 0.3158 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 7797 Z= 0.104 Angle : 0.464 5.931 10567 Z= 0.251 Chirality : 0.041 0.145 1214 Planarity : 0.003 0.049 1334 Dihedral : 3.872 16.642 1057 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.28 % Allowed : 22.86 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 955 helix: 2.14 (0.28), residues: 365 sheet: 0.37 (0.34), residues: 223 loop : -1.04 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 7 TYR 0.011 0.001 TYR R 277 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7795) covalent geometry : angle 0.46349 (10563) SS BOND : bond 0.00405 ( 2) SS BOND : angle 1.20273 ( 4) hydrogen bonds : bond 0.03902 ( 370) hydrogen bonds : angle 3.87862 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.322 Fit side-chains REVERT: R 57 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6233 (tp) REVERT: R 86 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6598 (mt) REVERT: R 199 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6991 (mpt) REVERT: R 264 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6630 (mp) REVERT: B 59 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: B 215 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7714 (mp0) REVERT: N 80 TYR cc_start: 0.8807 (m-80) cc_final: 0.8212 (m-80) REVERT: A 27 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 314 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: A 356 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7496 (mtm180) outliers start: 35 outliers final: 17 residues processed: 136 average time/residue: 0.4567 time to fit residues: 65.6730 Evaluate side-chains 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112058 restraints weight = 8667.213| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.12 r_work: 0.3136 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7797 Z= 0.124 Angle : 0.488 6.479 10567 Z= 0.262 Chirality : 0.042 0.135 1214 Planarity : 0.003 0.047 1334 Dihedral : 3.971 17.097 1057 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.52 % Allowed : 22.86 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.27), residues: 955 helix: 2.06 (0.28), residues: 365 sheet: 0.35 (0.34), residues: 223 loop : -1.05 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 7 TYR 0.012 0.001 TYR R 277 PHE 0.013 0.001 PHE B 241 TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7795) covalent geometry : angle 0.48725 (10563) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.29528 ( 4) hydrogen bonds : bond 0.04221 ( 370) hydrogen bonds : angle 3.97181 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.304 Fit side-chains REVERT: R 57 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6156 (tp) REVERT: R 199 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7109 (mpt) REVERT: R 264 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6609 (mp) REVERT: L 3 MET cc_start: 0.6680 (ttt) cc_final: 0.6391 (ttm) REVERT: B 23 LYS cc_start: 0.7665 (ttpp) cc_final: 0.7435 (ttmt) REVERT: B 59 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: N 80 TYR cc_start: 0.8849 (m-80) cc_final: 0.8336 (m-80) REVERT: A 27 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 314 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 356 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7499 (mtm180) outliers start: 37 outliers final: 23 residues processed: 135 average time/residue: 0.5143 time to fit residues: 73.3951 Evaluate side-chains 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 5 HIS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110574 restraints weight = 8592.726| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.02 r_work: 0.3122 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7797 Z= 0.156 Angle : 0.522 7.132 10567 Z= 0.279 Chirality : 0.043 0.148 1214 Planarity : 0.004 0.047 1334 Dihedral : 4.134 17.696 1057 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.40 % Allowed : 22.98 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 955 helix: 1.93 (0.28), residues: 366 sheet: 0.40 (0.34), residues: 217 loop : -1.12 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 7 TYR 0.015 0.001 TYR R 148 PHE 0.013 0.001 PHE B 241 TRP 0.012 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7795) covalent geometry : angle 0.52100 (10563) SS BOND : bond 0.00560 ( 2) SS BOND : angle 1.56563 ( 4) hydrogen bonds : bond 0.04661 ( 370) hydrogen bonds : angle 4.07594 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.170 Fit side-chains REVERT: R 57 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.6130 (tp) REVERT: R 199 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7088 (mpt) REVERT: R 264 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6662 (mp) REVERT: B 23 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7444 (ttmt) REVERT: B 59 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: N 80 TYR cc_start: 0.8865 (m-80) cc_final: 0.8363 (m-80) REVERT: A 27 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: A 314 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 356 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7520 (mtm180) outliers start: 36 outliers final: 24 residues processed: 137 average time/residue: 0.4854 time to fit residues: 70.2298 Evaluate side-chains 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111559 restraints weight = 8593.895| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.11 r_work: 0.3136 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7797 Z= 0.120 Angle : 0.483 6.465 10567 Z= 0.260 Chirality : 0.042 0.136 1214 Planarity : 0.003 0.047 1334 Dihedral : 4.002 17.433 1057 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.65 % Allowed : 22.74 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.27), residues: 955 helix: 2.04 (0.28), residues: 366 sheet: 0.42 (0.34), residues: 222 loop : -1.05 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 7 TYR 0.012 0.001 TYR R 148 PHE 0.013 0.001 PHE N 108 TRP 0.012 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7795) covalent geometry : angle 0.48248 (10563) SS BOND : bond 0.00452 ( 2) SS BOND : angle 1.47057 ( 4) hydrogen bonds : bond 0.04191 ( 370) hydrogen bonds : angle 3.96535 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.350 Fit side-chains REVERT: R 57 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6170 (tp) REVERT: R 199 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7089 (mpt) REVERT: R 264 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6610 (mp) REVERT: B 23 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7500 (ttmt) REVERT: B 59 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: N 80 TYR cc_start: 0.8856 (m-80) cc_final: 0.8301 (m-80) REVERT: A 27 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: A 314 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 356 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7521 (mtm180) outliers start: 38 outliers final: 22 residues processed: 139 average time/residue: 0.4530 time to fit residues: 66.6622 Evaluate side-chains 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114388 restraints weight = 8536.186| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.11 r_work: 0.3167 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7797 Z= 0.091 Angle : 0.451 5.513 10567 Z= 0.246 Chirality : 0.041 0.136 1214 Planarity : 0.003 0.045 1334 Dihedral : 3.805 16.534 1057 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 23.96 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.27), residues: 955 helix: 2.24 (0.28), residues: 364 sheet: 0.55 (0.34), residues: 220 loop : -1.04 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 10 TYR 0.010 0.001 TYR R 277 PHE 0.011 0.001 PHE B 241 TRP 0.012 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 7795) covalent geometry : angle 0.45052 (10563) SS BOND : bond 0.00375 ( 2) SS BOND : angle 1.18691 ( 4) hydrogen bonds : bond 0.03630 ( 370) hydrogen bonds : angle 3.81926 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.200 Fit side-chains REVERT: R 57 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6169 (tp) REVERT: R 86 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6623 (mt) REVERT: R 199 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6877 (mpt) REVERT: R 264 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6523 (mp) REVERT: B 23 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7442 (ttmt) REVERT: B 59 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: N 80 TYR cc_start: 0.8785 (m-80) cc_final: 0.8235 (m-80) REVERT: A 27 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 314 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 356 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7453 (mtm180) outliers start: 28 outliers final: 18 residues processed: 134 average time/residue: 0.4836 time to fit residues: 68.4884 Evaluate side-chains 139 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112796 restraints weight = 8573.763| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.12 r_work: 0.3144 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7797 Z= 0.117 Angle : 0.488 6.043 10567 Z= 0.263 Chirality : 0.041 0.137 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.885 16.955 1057 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.79 % Allowed : 23.96 % Favored : 72.25 % 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 aren not related in a simple way. whole: 0.86 (0.27), residues: 955 helix: 2.14 (0.28), residues: 366 sheet: 0.51 (0.34), residues: 222 loop : -1.03 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 10 TYR 0.011 0.001 TYR R 277 PHE 0.013 0.001 PHE N 108 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7795) covalent geometry : angle 0.48737 (10563) SS BOND : bond 0.00431 ( 2) SS BOND : angle 1.55776 ( 4) hydrogen bonds : bond 0.04002 ( 370) hydrogen bonds : angle 3.92589 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.218 Fit side-chains REVERT: R 57 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6200 (tp) REVERT: R 86 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6615 (mt) REVERT: R 199 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7057 (mpt) REVERT: R 264 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6599 (mp) REVERT: L 7 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7799 (ttm110) REVERT: B 23 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7462 (ttmt) REVERT: B 59 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: N 80 TYR cc_start: 0.8812 (m-80) cc_final: 0.8318 (m-80) REVERT: A 27 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: A 314 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 356 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7479 (mtm180) outliers start: 31 outliers final: 19 residues processed: 131 average time/residue: 0.4830 time to fit residues: 67.0000 Evaluate side-chains 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118798 restraints weight = 8648.837| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7797 Z= 0.134 Angle : 0.511 6.425 10567 Z= 0.276 Chirality : 0.042 0.138 1214 Planarity : 0.004 0.047 1334 Dihedral : 4.007 17.420 1057 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.67 % Allowed : 23.96 % Favored : 72.37 % 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 aren not related in a simple way. whole: 0.78 (0.27), residues: 955 helix: 2.05 (0.28), residues: 367 sheet: 0.47 (0.34), residues: 217 loop : -1.04 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 10 TYR 0.012 0.001 TYR R 148 PHE 0.014 0.001 PHE N 108 TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7795) covalent geometry : angle 0.51039 (10563) SS BOND : bond 0.00470 ( 2) SS BOND : angle 1.66695 ( 4) hydrogen bonds : bond 0.04297 ( 370) hydrogen bonds : angle 4.01269 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.83 seconds wall clock time: 40 minutes 29.44 seconds (2429.44 seconds total)