Starting phenix.real_space_refine on Fri Jun 6 10:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8y_37361/06_2025/8w8y_37361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8y_37361/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8y_37361/06_2025/8w8y_37361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8y_37361/06_2025/8w8y_37361.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8y_37361/06_2025/8w8y_37361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8y_37361/06_2025/8w8y_37361.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 7} 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: 4.87, per 1000 atoms: 0.64 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.04 Time building geometry restraints manager: 1.94 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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 : 7.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.002 PHE B 241 TYR 0.016 0.002 TYR R 277 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.18498 ( 370) hydrogen bonds : angle 6.37462 ( 1062) SS BOND : bond 0.00896 ( 2) SS BOND : angle 3.13382 ( 4) covalent geometry : bond 0.00529 ( 7795) covalent geometry : angle 0.62707 (10563) *********************** 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 : 0.804 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: 1.1719 time to fit residues: 174.9540 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 : 0.890 ------------------------------------------------------------------------------- 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 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110128 restraints weight = 8552.086| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.01 r_work: 0.3110 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7797 Z= 0.182 Angle : 0.564 7.288 10567 Z= 0.304 Chirality : 0.044 0.150 1214 Planarity : 0.004 0.064 1334 Dihedral : 5.752 50.435 1078 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.62 % Allowed : 20.29 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 955 helix: 1.45 (0.28), residues: 366 sheet: 0.09 (0.34), residues: 217 loop : -1.24 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.016 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.017 0.002 TYR R 148 ARG 0.003 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05689 ( 370) hydrogen bonds : angle 4.57265 ( 1062) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.35470 ( 4) covalent geometry : bond 0.00436 ( 7795) covalent geometry : angle 0.56339 (10563) *********************** 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 165 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.883 Fit side-chains REVERT: R 184 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: R 187 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7074 (tpp) REVERT: B 59 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: A 356 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7588 (mtm180) outliers start: 46 outliers final: 22 residues processed: 151 average time/residue: 1.1382 time to fit residues: 182.2880 Evaluate side-chains 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 238 MET 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 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 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 3 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN A 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111317 restraints weight = 8613.670| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3127 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7797 Z= 0.148 Angle : 0.523 7.442 10567 Z= 0.282 Chirality : 0.043 0.136 1214 Planarity : 0.004 0.055 1334 Dihedral : 4.412 25.973 1058 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.87 % Allowed : 21.03 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 955 helix: 1.65 (0.28), residues: 365 sheet: 0.18 (0.34), residues: 218 loop : -1.20 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 47 HIS 0.011 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.016 0.001 TYR N 80 ARG 0.003 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 370) hydrogen bonds : angle 4.30104 ( 1062) SS BOND : bond 0.00731 ( 2) SS BOND : angle 1.34404 ( 4) covalent geometry : bond 0.00354 ( 7795) covalent geometry : angle 0.52274 (10563) *********************** 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 166 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.835 Fit side-chains REVERT: R 184 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: R 187 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6883 (tpp) REVERT: R 199 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7167 (mpt) REVERT: R 264 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6824 (mp) REVERT: B 59 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: B 234 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: N 80 TYR cc_start: 0.8946 (m-80) cc_final: 0.8290 (m-80) REVERT: A 27 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 356 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7589 (mtm180) outliers start: 48 outliers final: 25 residues processed: 148 average time/residue: 1.1230 time to fit residues: 176.5750 Evaluate side-chains 148 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain R residue 184 GLU 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 263 VAL Chi-restraints excluded: chain R residue 264 LEU 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 134 ARG 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 234 PHE 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 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 320 THR Chi-restraints excluded: chain A residue 356 ARG 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 49 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.150671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110476 restraints weight = 8583.288| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7797 Z= 0.158 Angle : 0.528 7.518 10567 Z= 0.284 Chirality : 0.043 0.145 1214 Planarity : 0.004 0.052 1334 Dihedral : 4.328 18.082 1057 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.11 % Allowed : 21.76 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 955 helix: 1.66 (0.28), residues: 366 sheet: 0.18 (0.34), residues: 218 loop : -1.18 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.009 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.016 0.001 TYR R 148 ARG 0.003 0.000 ARG L 10 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 370) hydrogen bonds : angle 4.25657 ( 1062) SS BOND : bond 0.00600 ( 2) SS BOND : angle 1.32666 ( 4) covalent geometry : bond 0.00383 ( 7795) covalent geometry : angle 0.52715 (10563) *********************** 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 166 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.850 Fit side-chains REVERT: R 184 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: R 187 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6874 (tpp) REVERT: R 199 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7177 (mpt) REVERT: R 264 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6786 (mp) REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: B 234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: N 80 TYR cc_start: 0.8945 (m-80) cc_final: 0.8303 (m-80) REVERT: A 27 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: A 220 HIS cc_start: 0.8682 (t-170) cc_final: 0.8318 (t70) REVERT: A 314 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: A 356 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7578 (mtm180) outliers start: 50 outliers final: 24 residues processed: 146 average time/residue: 1.1123 time to fit residues: 172.5239 Evaluate side-chains 149 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 116 MET Chi-restraints excluded: chain R residue 184 GLU 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 263 VAL Chi-restraints excluded: chain R residue 264 LEU 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 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE 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 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 248 VAL Chi-restraints excluded: chain A residue 314 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.0030 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN B 340 ASN N 3 GLN A 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113413 restraints weight = 8613.921| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.08 r_work: 0.3153 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 7797 Z= 0.106 Angle : 0.473 6.207 10567 Z= 0.257 Chirality : 0.041 0.140 1214 Planarity : 0.003 0.049 1334 Dihedral : 4.047 17.158 1057 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.40 % Allowed : 23.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 955 helix: 1.98 (0.28), residues: 364 sheet: 0.26 (0.34), residues: 218 loop : -1.14 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR R 277 ARG 0.002 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 370) hydrogen bonds : angle 4.01433 ( 1062) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.20495 ( 4) covalent geometry : bond 0.00253 ( 7795) covalent geometry : angle 0.47281 (10563) *********************** 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 157 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.979 Fit side-chains REVERT: R 57 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6180 (tp) REVERT: R 199 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7046 (mpt) REVERT: R 264 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6675 (mp) REVERT: B 59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: N 80 TYR cc_start: 0.8885 (m-80) cc_final: 0.8309 (m-80) REVERT: A 27 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 314 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7826 (mp0) outliers start: 36 outliers final: 18 residues processed: 142 average time/residue: 1.1993 time to fit residues: 180.4348 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 : 0.862 ------------------------------------------------------------------------------- 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 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 146 LEU Chi-restraints excluded: chain B residue 189 SER 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 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112614 restraints weight = 8490.159| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7797 Z= 0.107 Angle : 0.474 6.147 10567 Z= 0.256 Chirality : 0.041 0.136 1214 Planarity : 0.003 0.047 1334 Dihedral : 3.952 17.084 1057 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.65 % Allowed : 22.86 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 955 helix: 2.05 (0.28), residues: 365 sheet: 0.39 (0.34), residues: 222 loop : -1.07 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR R 277 ARG 0.006 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 370) hydrogen bonds : angle 3.95447 ( 1062) SS BOND : bond 0.00369 ( 2) SS BOND : angle 1.27188 ( 4) covalent geometry : bond 0.00250 ( 7795) covalent geometry : angle 0.47335 (10563) *********************** 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: 38 poor density : 115 time to evaluate : 0.875 Fit side-chains REVERT: R 57 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6206 (tp) REVERT: R 199 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7080 (mpt) REVERT: R 264 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6648 (mp) REVERT: L 3 MET cc_start: 0.6712 (ttt) cc_final: 0.6440 (ttm) REVERT: B 23 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7441 (ttmt) REVERT: B 59 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: B 215 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: N 80 TYR cc_start: 0.8839 (m-80) cc_final: 0.8254 (m-80) REVERT: A 27 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 314 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7824 (mp0) outliers start: 38 outliers final: 20 residues processed: 135 average time/residue: 1.2555 time to fit residues: 179.1713 Evaluate side-chains 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 87 VAL 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 215 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 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 = 0.3733 r_free = 0.3733 target = 0.152263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111730 restraints weight = 8492.229| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.11 r_work: 0.3138 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7797 Z= 0.118 Angle : 0.482 6.398 10567 Z= 0.260 Chirality : 0.042 0.139 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.995 17.242 1057 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.89 % Allowed : 22.62 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 955 helix: 2.03 (0.28), residues: 366 sheet: 0.41 (0.34), residues: 217 loop : -1.09 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR R 277 ARG 0.004 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 370) hydrogen bonds : angle 3.96053 ( 1062) SS BOND : bond 0.00441 ( 2) SS BOND : angle 1.36435 ( 4) covalent geometry : bond 0.00278 ( 7795) covalent geometry : angle 0.48166 (10563) *********************** 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 155 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.941 Fit side-chains REVERT: R 57 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6195 (tp) REVERT: R 199 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7092 (mpt) REVERT: R 264 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6594 (mp) REVERT: L 3 MET cc_start: 0.6693 (ttt) cc_final: 0.6424 (ttm) REVERT: B 23 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7446 (ttmt) REVERT: B 59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: B 215 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: N 80 TYR cc_start: 0.8850 (m-80) cc_final: 0.8278 (m-80) REVERT: A 27 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 314 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 356 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7547 (mtm180) outliers start: 40 outliers final: 23 residues processed: 140 average time/residue: 1.1440 time to fit residues: 170.2143 Evaluate side-chains 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain R residue 155 ILE 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 215 GLU 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 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR 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 45 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 0.0030 chunk 73 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 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 = 0.3746 r_free = 0.3746 target = 0.153705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113258 restraints weight = 8621.348| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.12 r_work: 0.3149 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7797 Z= 0.103 Angle : 0.465 5.989 10567 Z= 0.252 Chirality : 0.041 0.136 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.887 16.870 1057 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.65 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 955 helix: 2.08 (0.28), residues: 367 sheet: 0.46 (0.34), residues: 222 loop : -1.02 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.010 0.001 TYR R 277 ARG 0.003 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 370) hydrogen bonds : angle 3.87736 ( 1062) SS BOND : bond 0.00636 ( 2) SS BOND : angle 1.46901 ( 4) covalent geometry : bond 0.00235 ( 7795) covalent geometry : angle 0.46399 (10563) *********************** 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 151 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.984 Fit side-chains REVERT: R 57 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6172 (tp) REVERT: R 86 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6650 (mt) REVERT: R 199 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6997 (mpt) REVERT: R 264 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6598 (mp) REVERT: L 3 MET cc_start: 0.6625 (ttt) cc_final: 0.6384 (ttm) REVERT: B 23 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7448 (ttmt) REVERT: B 59 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: B 340 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7180 (m110) REVERT: N 80 TYR cc_start: 0.8824 (m-80) cc_final: 0.8253 (m-80) REVERT: A 27 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 314 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: A 356 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7501 (mtm180) outliers start: 38 outliers final: 21 residues processed: 133 average time/residue: 1.5431 time to fit residues: 218.2100 Evaluate side-chains 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 208 VAL 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 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 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN 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 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 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 = 0.3761 r_free = 0.3761 target = 0.155096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114755 restraints weight = 8648.517| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.13 r_work: 0.3157 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7797 Z= 0.091 Angle : 0.454 5.608 10567 Z= 0.247 Chirality : 0.040 0.143 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.792 16.363 1057 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 24.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 955 helix: 2.20 (0.28), residues: 367 sheet: 0.57 (0.35), residues: 216 loop : -1.00 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR R 277 ARG 0.004 0.000 ARG L 10 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 370) hydrogen bonds : angle 3.81161 ( 1062) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.16813 ( 4) covalent geometry : bond 0.00198 ( 7795) covalent geometry : angle 0.45330 (10563) *********************** 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 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.831 Fit side-chains REVERT: R 57 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6256 (tp) REVERT: R 86 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6639 (mt) REVERT: R 264 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6533 (mp) REVERT: B 23 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7454 (ttmt) REVERT: B 59 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: B 325 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (tpp) REVERT: N 80 TYR cc_start: 0.8804 (m-80) cc_final: 0.8239 (m-80) REVERT: A 27 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: A 314 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 356 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7499 (mtm180) outliers start: 28 outliers final: 17 residues processed: 129 average time/residue: 1.2647 time to fit residues: 172.4105 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 : 0.798 ------------------------------------------------------------------------------- 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 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 189 SER 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 113 THR 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 24 optimal weight: 0.0050 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 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 = 0.3759 r_free = 0.3759 target = 0.154872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114482 restraints weight = 8573.254| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.11 r_work: 0.3165 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1784 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= 0.098 Angle : 0.464 5.617 10567 Z= 0.251 Chirality : 0.041 0.134 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.775 16.502 1057 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 24.45 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 955 helix: 2.26 (0.28), residues: 366 sheet: 0.60 (0.35), residues: 216 loop : -1.03 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.010 0.001 TYR R 277 ARG 0.004 0.000 ARG L 10 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 370) hydrogen bonds : angle 3.81265 ( 1062) SS BOND : bond 0.00373 ( 2) SS BOND : angle 1.24928 ( 4) covalent geometry : bond 0.00220 ( 7795) covalent geometry : angle 0.46386 (10563) ********************** 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 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.754 Fit side-chains REVERT: R 57 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6229 (tp) REVERT: R 86 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6625 (mt) REVERT: R 264 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6572 (mp) REVERT: B 23 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7458 (ttmt) REVERT: B 59 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: N 80 TYR cc_start: 0.8811 (m-80) cc_final: 0.8248 (m-80) REVERT: A 27 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: A 314 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 356 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7504 (mtm180) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 1.2530 time to fit residues: 168.1212 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 59 TYR Chi-restraints excluded: chain B residue 67 SER 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 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN A 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113856 restraints weight = 8611.516| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.13 r_work: 0.3153 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7797 Z= 0.107 Angle : 0.473 5.848 10567 Z= 0.256 Chirality : 0.041 0.133 1214 Planarity : 0.003 0.046 1334 Dihedral : 3.819 16.699 1057 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 24.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 955 helix: 2.24 (0.28), residues: 366 sheet: 0.60 (0.35), residues: 211 loop : -1.03 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR R 277 ARG 0.004 0.000 ARG L 10 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 370) hydrogen bonds : angle 3.86184 ( 1062) SS BOND : bond 0.00401 ( 2) SS BOND : angle 1.30458 ( 4) covalent geometry : bond 0.00247 ( 7795) covalent geometry : angle 0.47237 (10563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.74 seconds wall clock time: 112 minutes 39.00 seconds (6759.00 seconds total)