Starting phenix.real_space_refine on Thu Jul 2 19:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb5_64916/07_2026/9vb5_64916.cif" } resolution = 3.14 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= -0.006 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 6273 2.51 5 N 1686 2.21 5 O 1850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9874 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2265 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2778 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 345} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9874 At special positions: 0 Unit cell: (98.2167, 118.967, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 2 15.00 O 1850 8.00 N 1686 7.00 C 6273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.08 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.06 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: 0.67 Conformation dependent library (CDL) restraints added in 223.0 milliseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 42.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 61 through 90 removed outlier: 3.526A pdb=" N THR R 67 " --> pdb=" O LYS R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 129 removed outlier: 4.154A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.893A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 206 removed outlier: 3.732A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Proline residue: R 202 - end of helix removed outlier: 3.546A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 222 Processing helix chain 'R' and resid 229 through 273 removed outlier: 6.051A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 330 through 334 Processing helix chain 'R' and resid 335 through 336 No H-bonds generated for 'chain 'R' and resid 335 through 336' Processing helix chain 'R' and resid 337 through 365 removed outlier: 3.992A pdb=" N PHE R 341 " --> pdb=" O PHE R 337 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR R 342 " --> pdb=" O LEU R 338 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HIS R 343 " --> pdb=" O TYR R 339 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 375 Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.880A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.729A pdb=" N TYR A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.834A pdb=" N TYR A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.844A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.519A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.066A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.055A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.138A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 345 removed outlier: 3.705A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.660A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.511A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.029A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 210 removed outlier: 4.131A pdb=" N GLY R 208 " --> pdb=" O THR R 225 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR R 225 " --> pdb=" O GLY R 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL R 223 " --> pdb=" O GLN R 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.041A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 320 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.301A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.768A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.638A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.709A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.686A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.522A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.527A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 3.724A pdb=" N GLN D 167 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1664 1.32 - 1.45: 2742 1.45 - 1.57: 5571 1.57 - 1.70: 6 1.70 - 1.82: 95 Bond restraints: 10078 Sorted by residual: bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.529 1.316 0.214 1.78e-02 3.16e+03 1.44e+02 bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.596 -0.212 2.10e-02 2.27e+03 1.02e+02 bond pdb=" CB LYS R 186 " pdb=" CG LYS R 186 " ideal model delta sigma weight residual 1.520 1.724 -0.204 3.00e-02 1.11e+03 4.61e+01 bond pdb=" CG1 ILE R 237 " pdb=" CD1 ILE R 237 " ideal model delta sigma weight residual 1.513 1.777 -0.264 3.90e-02 6.57e+02 4.58e+01 bond pdb=" CB VAL R 239 " pdb=" CG2 VAL R 239 " ideal model delta sigma weight residual 1.521 1.310 0.211 3.30e-02 9.18e+02 4.08e+01 ... (remaining 10073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 12636 3.62 - 7.23: 961 7.23 - 10.85: 65 10.85 - 14.47: 10 14.47 - 18.08: 5 Bond angle restraints: 13677 Sorted by residual: angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" CB TYR B 59 " ideal model delta sigma weight residual 110.40 92.32 18.08 1.45e+00 4.76e-01 1.56e+02 angle pdb=" CA VAL R 239 " pdb=" CB VAL R 239 " pdb=" CG1 VAL R 239 " ideal model delta sigma weight residual 110.40 93.93 16.47 1.70e+00 3.46e-01 9.39e+01 angle pdb=" N VAL R 251 " pdb=" CA VAL R 251 " pdb=" CB VAL R 251 " ideal model delta sigma weight residual 110.55 119.73 -9.18 1.17e+00 7.31e-01 6.15e+01 angle pdb=" N TYR D 178 " pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " ideal model delta sigma weight residual 111.62 124.10 -12.48 1.62e+00 3.81e-01 5.94e+01 angle pdb=" N VAL A 339 " pdb=" CA VAL A 339 " pdb=" CB VAL A 339 " ideal model delta sigma weight residual 110.62 118.78 -8.16 1.09e+00 8.42e-01 5.61e+01 ... (remaining 13672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 5588 25.98 - 51.95: 304 51.95 - 77.92: 62 77.92 - 103.90: 10 103.90 - 129.87: 1 Dihedral angle restraints: 5965 sinusoidal: 2259 harmonic: 3706 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 170.06 -77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CD ARG R 182 " pdb=" NE ARG R 182 " pdb=" CZ ARG R 182 " pdb=" NH1 ARG R 182 " ideal model delta sinusoidal sigma weight residual 0.00 -74.65 74.65 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" C SER R 330 " pdb=" N SER R 330 " pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta harmonic sigma weight residual -122.60 -142.01 19.41 0 2.50e+00 1.60e-01 6.03e+01 ... (remaining 5962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1437 0.196 - 0.392: 122 0.392 - 0.587: 5 0.587 - 0.783: 1 0.783 - 0.979: 1 Chirality restraints: 1566 Sorted by residual: chirality pdb=" CG LEU R 118 " pdb=" CB LEU R 118 " pdb=" CD1 LEU R 118 " pdb=" CD2 LEU R 118 " both_signs ideal model delta sigma weight residual False -2.59 -1.61 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA SER R 330 " pdb=" N SER R 330 " pdb=" C SER R 330 " pdb=" CB SER R 330 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA ARG D 179 " pdb=" N ARG D 179 " pdb=" C ARG D 179 " pdb=" CB ARG D 179 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.60e+00 ... (remaining 1563 not shown) Planarity restraints: 1727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " 1.095 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG R 182 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 242 " -0.710 9.50e-02 1.11e+02 3.24e-01 1.11e+02 pdb=" NE ARG A 242 " 0.084 2.00e-02 2.50e+03 pdb=" CZ ARG A 242 " -0.114 2.00e-02 2.50e+03 pdb=" NH1 ARG A 242 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 242 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " 0.369 9.50e-02 1.11e+02 1.71e-01 4.17e+01 pdb=" NE ARG A 205 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " -0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " 0.041 2.00e-02 2.50e+03 ... (remaining 1724 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 115 2.65 - 3.21: 8785 3.21 - 3.77: 15610 3.77 - 4.34: 21168 4.34 - 4.90: 34936 Nonbonded interactions: 80614 Sorted by model distance: nonbonded pdb=" OG SER D 149 " pdb=" O LYS D 151 " model vdw 2.083 3.040 nonbonded pdb=" O TYR R 364 " pdb=" OG SER R 368 " model vdw 2.156 3.040 nonbonded pdb=" O ASN A 241 " pdb=" N HIS A 244 " model vdw 2.232 3.120 nonbonded pdb=" O ASP D 211 " pdb=" OH TYR D 215 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR A 155 " pdb=" O ASP A 173 " model vdw 2.326 3.040 ... (remaining 80609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.012 0.264 10081 Z= 0.739 Angle : 2.072 18.083 13683 Z= 1.378 Chirality : 0.119 0.979 1566 Planarity : 0.019 0.491 1727 Dihedral : 17.128 129.874 3566 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.99 % Allowed : 9.19 % Favored : 83.83 % Cbeta Deviations : 1.42 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.20), residues: 1255 helix: -2.19 (0.19), residues: 450 sheet: -1.40 (0.35), residues: 200 loop : -1.99 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.122 0.008 ARG A 242 TYR 0.069 0.006 TYR D 178 PHE 0.031 0.005 PHE R 353 TRP 0.080 0.007 TRP R 134 HIS 0.019 0.004 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01217 / 0.74 (10078) covalent geometry : angle 2.07162 / 1.38 (13677) SS BOND : bond 0.03515 / 1.70 ( 3) SS BOND : angle 3.08711 / 1.67 ( 6) hydrogen bonds : bond 0.21926 / 15.29 ( 501) hydrogen bonds : angle 8.56722 / 6.38 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 318 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: 0.9194 (tpt) cc_final: 0.8856 (tpt) REVERT: R 136 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8752 (t80) REVERT: R 172 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6742 (m-70) REVERT: R 207 MET cc_start: 0.8220 (mmp) cc_final: 0.7605 (mmm) REVERT: A 14 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 21 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8321 (ttm170) REVERT: A 144 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8577 (ttp80) REVERT: A 179 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7601 (m) REVERT: A 199 PHE cc_start: 0.8710 (m-80) cc_final: 0.8296 (m-80) REVERT: A 238 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: A 248 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9292 (mttp) REVERT: A 256 ASN cc_start: 0.9074 (t0) cc_final: 0.8560 (t0) REVERT: A 304 GLN cc_start: 0.8918 (tt0) cc_final: 0.8171 (tt0) REVERT: B 15 LYS cc_start: 0.8239 (tttp) cc_final: 0.7845 (mmmm) REVERT: B 19 ARG cc_start: 0.9120 (tmt90) cc_final: 0.8566 (ttp-110) REVERT: B 54 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.6064 (m-70) REVERT: B 226 GLU cc_start: 0.9084 (mp0) cc_final: 0.8833 (mp0) REVERT: B 333 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8681 (p0) REVERT: C 19 LEU cc_start: 0.9138 (mt) cc_final: 0.8741 (mt) REVERT: C 58 GLU cc_start: 0.8773 (tp30) cc_final: 0.8553 (tp30) REVERT: D 39 GLN cc_start: 0.7970 (tt0) cc_final: 0.7517 (tt0) REVERT: D 125 ASP cc_start: 0.8326 (m-30) cc_final: 0.7954 (m-30) REVERT: D 143 VAL cc_start: 0.7879 (t) cc_final: 0.7559 (t) REVERT: D 166 LEU cc_start: 0.8623 (tp) cc_final: 0.8304 (tp) REVERT: D 168 ARG cc_start: 0.8169 (mpp80) cc_final: 0.7931 (mtp180) REVERT: D 171 GLN cc_start: 0.7889 (mt0) cc_final: 0.7477 (mp10) REVERT: D 172 SER cc_start: 0.8717 (m) cc_final: 0.8090 (t) REVERT: D 174 GLN cc_start: 0.8326 (pt0) cc_final: 0.8091 (mp10) REVERT: D 180 MET cc_start: 0.7233 (ttm) cc_final: 0.6909 (tmm) REVERT: D 218 MET cc_start: 0.8691 (ttp) cc_final: 0.8426 (ttt) outliers start: 73 outliers final: 21 residues processed: 372 average time/residue: 0.0988 time to fit residues: 49.0388 Evaluate side-chains 232 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 172 HIS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 178 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 104 HIS R 296 GLN R 350 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 HIS A 141 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 322 HIS B 75 GLN B 88 ASN B 91 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 340 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.118385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.092595 restraints weight = 25642.558| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.91 r_work: 0.3469 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10081 Z= 0.165 Angle : 0.769 12.599 13683 Z= 0.395 Chirality : 0.046 0.203 1566 Planarity : 0.005 0.038 1727 Dihedral : 9.346 100.122 1457 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.69 % Allowed : 18.56 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1255 helix: 0.40 (0.22), residues: 471 sheet: -0.84 (0.30), residues: 275 loop : -1.74 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 148 TYR 0.026 0.002 TYR A 61 PHE 0.018 0.002 PHE A 336 TRP 0.028 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10078) covalent geometry : angle 0.76808 / 0.39 (13677) SS BOND : bond 0.00727 / 0.35 ( 3) SS BOND : angle 2.34714 / 1.02 ( 6) hydrogen bonds : bond 0.05303 / 3.69 ( 501) hydrogen bonds : angle 5.82466 / 4.36 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: 0.9262 (tpt) cc_final: 0.8972 (mmt) REVERT: R 136 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8523 (t80) REVERT: R 184 ARG cc_start: 0.8425 (tpt170) cc_final: 0.8092 (tpt170) REVERT: A 21 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7901 (ttm170) REVERT: A 130 LEU cc_start: 0.8997 (mp) cc_final: 0.8709 (mm) REVERT: A 219 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 238 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: A 247 MET cc_start: 0.9043 (mtt) cc_final: 0.8646 (mtm) REVERT: A 256 ASN cc_start: 0.8847 (t0) cc_final: 0.8076 (t0) REVERT: A 277 LYS cc_start: 0.6731 (mtpp) cc_final: 0.6369 (ttmm) REVERT: A 308 GLU cc_start: 0.7130 (pt0) cc_final: 0.6773 (mt-10) REVERT: A 320 TYR cc_start: 0.8788 (m-10) cc_final: 0.8518 (m-10) REVERT: B 19 ARG cc_start: 0.8825 (tmt90) cc_final: 0.8512 (ttp-110) REVERT: B 61 MET cc_start: 0.8845 (tmm) cc_final: 0.8528 (ppp) REVERT: B 105 TYR cc_start: 0.8312 (t80) cc_final: 0.8068 (t80) REVERT: B 142 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7762 (t-170) REVERT: B 226 GLU cc_start: 0.8960 (mp0) cc_final: 0.8612 (mp0) REVERT: B 268 ASN cc_start: 0.9208 (m-40) cc_final: 0.8925 (p0) REVERT: B 294 CYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8049 (t) REVERT: B 311 HIS cc_start: 0.6911 (m-70) cc_final: 0.6343 (m-70) REVERT: B 329 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8410 (p) REVERT: C 14 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8335 (mmtm) REVERT: C 22 GLU cc_start: 0.8489 (tp30) cc_final: 0.8087 (tm-30) REVERT: C 29 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8776 (mmmt) REVERT: C 58 GLU cc_start: 0.8815 (tp30) cc_final: 0.8328 (tp30) REVERT: D 19 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8107 (mptm) REVERT: D 148 ARG cc_start: 0.7929 (mpp80) cc_final: 0.7562 (mpp80) REVERT: D 171 GLN cc_start: 0.7287 (mt0) cc_final: 0.6956 (mp10) REVERT: D 174 GLN cc_start: 0.8218 (pt0) cc_final: 0.7769 (mp10) REVERT: D 180 MET cc_start: 0.6973 (ttm) cc_final: 0.6538 (tmm) REVERT: D 211 ASP cc_start: 0.8832 (m-30) cc_final: 0.8442 (t0) REVERT: D 218 MET cc_start: 0.8642 (ttp) cc_final: 0.8018 (ttt) outliers start: 49 outliers final: 16 residues processed: 257 average time/residue: 0.0915 time to fit residues: 31.6874 Evaluate side-chains 198 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN B 13 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.109986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.084426 restraints weight = 26427.420| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.93 r_work: 0.3328 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10081 Z= 0.256 Angle : 0.770 9.408 13683 Z= 0.400 Chirality : 0.047 0.253 1566 Planarity : 0.005 0.043 1727 Dihedral : 7.398 101.506 1402 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.55 % Allowed : 19.04 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1255 helix: 0.70 (0.22), residues: 472 sheet: -1.01 (0.29), residues: 273 loop : -1.54 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.028 0.002 TYR D 178 PHE 0.024 0.002 PHE R 345 TRP 0.020 0.002 TRP R 134 HIS 0.006 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (10078) covalent geometry : angle 0.76520 / 0.40 (13677) SS BOND : bond 0.01766 / 0.85 ( 3) SS BOND : angle 4.08385 / 1.75 ( 6) hydrogen bonds : bond 0.05336 / 3.65 ( 501) hydrogen bonds : angle 5.69163 / 4.29 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 136 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8551 (t80) REVERT: R 266 MET cc_start: 0.8208 (ptt) cc_final: 0.7965 (ppp) REVERT: R 343 HIS cc_start: 0.9141 (m90) cc_final: 0.8469 (m-70) REVERT: R 363 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8334 (tp) REVERT: R 364 TYR cc_start: 0.8488 (m-80) cc_final: 0.8285 (m-80) REVERT: L 12 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 21 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7870 (ttm170) REVERT: A 130 LEU cc_start: 0.9314 (mp) cc_final: 0.9046 (mm) REVERT: A 219 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 238 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: A 256 ASN cc_start: 0.8900 (t0) cc_final: 0.8251 (t0) REVERT: A 277 LYS cc_start: 0.6937 (mtpp) cc_final: 0.6536 (ttmm) REVERT: B 19 ARG cc_start: 0.8887 (tmt90) cc_final: 0.8602 (ttp-110) REVERT: B 105 TYR cc_start: 0.8432 (t80) cc_final: 0.8112 (t80) REVERT: B 142 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7843 (t-170) REVERT: B 226 GLU cc_start: 0.8948 (mp0) cc_final: 0.8570 (mp0) REVERT: B 262 MET cc_start: 0.8610 (tpp) cc_final: 0.8182 (tpp) REVERT: C 14 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8434 (mmtt) REVERT: C 22 GLU cc_start: 0.8619 (tp30) cc_final: 0.8291 (tm-30) REVERT: C 58 GLU cc_start: 0.8863 (tp30) cc_final: 0.8364 (tp30) REVERT: D 42 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9046 (mm-30) REVERT: D 55 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7117 (p) REVERT: D 148 ARG cc_start: 0.8152 (mpp80) cc_final: 0.7673 (mpp80) REVERT: D 171 GLN cc_start: 0.7404 (mt0) cc_final: 0.6953 (mp10) REVERT: D 180 MET cc_start: 0.7037 (ttm) cc_final: 0.6662 (tmm) REVERT: D 211 ASP cc_start: 0.8907 (m-30) cc_final: 0.8647 (t0) outliers start: 58 outliers final: 34 residues processed: 228 average time/residue: 0.0890 time to fit residues: 27.9813 Evaluate side-chains 206 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 244 HIS B 88 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.112412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086851 restraints weight = 25849.846| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.93 r_work: 0.3382 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10081 Z= 0.156 Angle : 0.699 12.757 13683 Z= 0.353 Chirality : 0.043 0.185 1566 Planarity : 0.004 0.037 1727 Dihedral : 6.846 91.518 1401 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.88 % Allowed : 20.29 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.23), residues: 1255 helix: 1.09 (0.23), residues: 476 sheet: -0.87 (0.30), residues: 271 loop : -1.28 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.022 0.002 TYR D 178 PHE 0.020 0.002 PHE R 345 TRP 0.015 0.002 TRP B 297 HIS 0.004 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10078) covalent geometry : angle 0.69790 / 0.35 (13677) SS BOND : bond 0.00941 / 0.46 ( 3) SS BOND : angle 2.23080 / 0.92 ( 6) hydrogen bonds : bond 0.04545 / 3.12 ( 501) hydrogen bonds : angle 5.35747 / 4.04 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8463 (mmm) REVERT: R 136 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8382 (t80) REVERT: R 184 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.7944 (tpp-160) REVERT: R 203 MET cc_start: 0.7945 (tpp) cc_final: 0.7725 (tpp) REVERT: R 266 MET cc_start: 0.8232 (ptt) cc_final: 0.7987 (ppp) REVERT: R 363 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8231 (tp) REVERT: R 364 TYR cc_start: 0.8618 (m-80) cc_final: 0.8341 (m-80) REVERT: A 21 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.7818 (ttm170) REVERT: A 130 LEU cc_start: 0.9292 (mp) cc_final: 0.9041 (mm) REVERT: A 219 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 238 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: A 248 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9033 (mttt) REVERT: A 256 ASN cc_start: 0.8863 (t0) cc_final: 0.8250 (t0) REVERT: A 277 LYS cc_start: 0.6759 (mtpp) cc_final: 0.6374 (ttmt) REVERT: A 308 GLU cc_start: 0.7034 (pt0) cc_final: 0.6600 (pt0) REVERT: B 105 TYR cc_start: 0.8424 (t80) cc_final: 0.8106 (t80) REVERT: B 142 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7866 (t-170) REVERT: B 226 GLU cc_start: 0.8842 (mp0) cc_final: 0.8428 (mp0) REVERT: B 325 MET cc_start: 0.8882 (mmm) cc_final: 0.8591 (mmm) REVERT: B 340 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7643 (t0) REVERT: C 14 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8469 (mmtt) REVERT: C 22 GLU cc_start: 0.8646 (tp30) cc_final: 0.8304 (tm-30) REVERT: C 29 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8848 (mmmt) REVERT: C 58 GLU cc_start: 0.8880 (tp30) cc_final: 0.8372 (tp30) REVERT: D 38 ARG cc_start: 0.8376 (ptt-90) cc_final: 0.7963 (ptt-90) REVERT: D 42 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8961 (mm-30) REVERT: D 55 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7326 (p) REVERT: D 93 MET cc_start: 0.7495 (tpp) cc_final: 0.7243 (tpp) REVERT: D 148 ARG cc_start: 0.8276 (mpp80) cc_final: 0.7985 (mpp80) REVERT: D 171 GLN cc_start: 0.7525 (mt0) cc_final: 0.7016 (mp10) REVERT: D 218 MET cc_start: 0.8682 (ttt) cc_final: 0.8158 (ttt) outliers start: 51 outliers final: 27 residues processed: 227 average time/residue: 0.0927 time to fit residues: 28.7090 Evaluate side-chains 205 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.112079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086573 restraints weight = 25723.253| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.86 r_work: 0.3381 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10081 Z= 0.161 Angle : 0.689 11.933 13683 Z= 0.347 Chirality : 0.044 0.249 1566 Planarity : 0.004 0.047 1727 Dihedral : 6.584 86.400 1401 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.69 % Allowed : 21.15 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1255 helix: 1.26 (0.23), residues: 477 sheet: -0.87 (0.30), residues: 273 loop : -1.11 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.021 0.001 TYR D 178 PHE 0.018 0.002 PHE R 345 TRP 0.012 0.002 TRP R 134 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10078) covalent geometry : angle 0.68833 / 0.35 (13677) SS BOND : bond 0.00933 / 0.45 ( 3) SS BOND : angle 1.90401 / 0.80 ( 6) hydrogen bonds : bond 0.04419 / 3.00 ( 501) hydrogen bonds : angle 5.27050 / 3.99 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 ASP cc_start: 0.9435 (m-30) cc_final: 0.9207 (m-30) REVERT: R 120 MET cc_start: 0.8992 (tpt) cc_final: 0.8397 (mmt) REVERT: R 136 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8302 (t80) REVERT: R 184 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.7877 (tpp-160) REVERT: R 203 MET cc_start: 0.8075 (tpp) cc_final: 0.7826 (tpp) REVERT: R 249 MET cc_start: 0.7203 (mmm) cc_final: 0.6947 (mmm) REVERT: R 266 MET cc_start: 0.8323 (ptt) cc_final: 0.8086 (ppp) REVERT: R 346 TYR cc_start: 0.8771 (t80) cc_final: 0.8488 (t80) REVERT: R 363 LEU cc_start: 0.8587 (mp) cc_final: 0.8312 (tp) REVERT: A 21 ARG cc_start: 0.8391 (ttp-170) cc_final: 0.7829 (ttm170) REVERT: A 130 LEU cc_start: 0.9314 (mp) cc_final: 0.9069 (mm) REVERT: A 207 GLU cc_start: 0.8822 (tp30) cc_final: 0.8041 (tm-30) REVERT: A 219 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8302 (t) REVERT: A 244 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8091 (m90) REVERT: A 248 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9021 (mttt) REVERT: A 256 ASN cc_start: 0.8887 (t0) cc_final: 0.8384 (t0) REVERT: A 308 GLU cc_start: 0.7144 (pt0) cc_final: 0.6609 (pt0) REVERT: A 341 ASP cc_start: 0.9363 (t0) cc_final: 0.9067 (m-30) REVERT: B 45 MET cc_start: 0.8420 (mtp) cc_final: 0.7814 (mmm) REVERT: B 105 TYR cc_start: 0.8449 (t80) cc_final: 0.8124 (t80) REVERT: B 127 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8636 (mttp) REVERT: B 142 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7953 (t-170) REVERT: B 226 GLU cc_start: 0.8834 (mp0) cc_final: 0.8250 (mp0) REVERT: C 14 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8537 (mmtm) REVERT: C 22 GLU cc_start: 0.8710 (tp30) cc_final: 0.8307 (tm-30) REVERT: C 29 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9037 (mmmt) REVERT: C 58 GLU cc_start: 0.8983 (tp30) cc_final: 0.8583 (tp30) REVERT: D 46 GLU cc_start: 0.8078 (tt0) cc_final: 0.7660 (pt0) REVERT: D 55 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7353 (p) REVERT: D 93 MET cc_start: 0.7556 (tpp) cc_final: 0.7227 (tpp) REVERT: D 148 ARG cc_start: 0.8303 (mpp80) cc_final: 0.8011 (mpp80) REVERT: D 171 GLN cc_start: 0.7551 (mt0) cc_final: 0.7010 (mp10) REVERT: D 180 MET cc_start: 0.7682 (tpp) cc_final: 0.6441 (tpp) REVERT: D 211 ASP cc_start: 0.8769 (t0) cc_final: 0.8098 (t0) REVERT: D 218 MET cc_start: 0.8690 (ttt) cc_final: 0.8245 (ttt) outliers start: 49 outliers final: 30 residues processed: 222 average time/residue: 0.0867 time to fit residues: 26.1241 Evaluate side-chains 207 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.112742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087213 restraints weight = 25686.822| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.93 r_work: 0.3395 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10081 Z= 0.145 Angle : 0.675 11.738 13683 Z= 0.341 Chirality : 0.044 0.188 1566 Planarity : 0.004 0.037 1727 Dihedral : 5.989 81.423 1398 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.59 % Allowed : 22.78 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1255 helix: 1.38 (0.23), residues: 484 sheet: -0.76 (0.30), residues: 269 loop : -1.13 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.020 0.001 TYR D 178 PHE 0.017 0.001 PHE R 353 TRP 0.013 0.001 TRP B 297 HIS 0.005 0.001 HIS R 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10078) covalent geometry : angle 0.67413 / 0.34 (13677) SS BOND : bond 0.00845 / 0.41 ( 3) SS BOND : angle 1.65257 / 0.69 ( 6) hydrogen bonds : bond 0.04181 / 2.83 ( 501) hydrogen bonds : angle 5.16657 / 3.89 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 ASP cc_start: 0.9434 (m-30) cc_final: 0.9231 (m-30) REVERT: R 120 MET cc_start: 0.8884 (tpt) cc_final: 0.8295 (mmt) REVERT: R 136 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8251 (t80) REVERT: R 184 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.8018 (tpp-160) REVERT: R 203 MET cc_start: 0.8100 (tpp) cc_final: 0.7827 (tpp) REVERT: R 249 MET cc_start: 0.7714 (mmm) cc_final: 0.7452 (mmm) REVERT: R 263 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7740 (mp) REVERT: R 305 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8618 (mp) REVERT: R 316 TRP cc_start: 0.6209 (m100) cc_final: 0.5641 (m100) REVERT: A 21 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7779 (ttm170) REVERT: A 205 ARG cc_start: 0.8679 (mmt90) cc_final: 0.8359 (mmt180) REVERT: A 207 GLU cc_start: 0.8825 (tp30) cc_final: 0.8146 (tm-30) REVERT: A 219 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8142 (t) REVERT: A 244 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8072 (m170) REVERT: A 248 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9029 (mttt) REVERT: A 256 ASN cc_start: 0.8887 (t0) cc_final: 0.8386 (t0) REVERT: A 257 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8924 (ttpp) REVERT: A 308 GLU cc_start: 0.7077 (pt0) cc_final: 0.6569 (pt0) REVERT: B 45 MET cc_start: 0.8494 (mtp) cc_final: 0.7770 (mmm) REVERT: B 105 TYR cc_start: 0.8500 (t80) cc_final: 0.8235 (t80) REVERT: B 142 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7868 (t-170) REVERT: B 148 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 226 GLU cc_start: 0.8807 (mp0) cc_final: 0.8181 (mp0) REVERT: B 325 MET cc_start: 0.8811 (mmm) cc_final: 0.8421 (mmm) REVERT: C 14 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8546 (mmtt) REVERT: C 22 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: C 29 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9018 (mmmt) REVERT: C 58 GLU cc_start: 0.9026 (tp30) cc_final: 0.8681 (tp30) REVERT: D 46 GLU cc_start: 0.8161 (tt0) cc_final: 0.7596 (pt0) REVERT: D 80 PHE cc_start: 0.7504 (m-80) cc_final: 0.7128 (m-80) REVERT: D 93 MET cc_start: 0.7716 (tpp) cc_final: 0.7461 (tpp) REVERT: D 171 GLN cc_start: 0.7644 (mt0) cc_final: 0.6989 (mp-120) REVERT: D 211 ASP cc_start: 0.8956 (t0) cc_final: 0.8168 (t0) REVERT: D 218 MET cc_start: 0.8683 (ttt) cc_final: 0.8266 (ttt) outliers start: 48 outliers final: 28 residues processed: 219 average time/residue: 0.0909 time to fit residues: 27.3709 Evaluate side-chains 207 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 70 optimal weight: 0.0570 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.085154 restraints weight = 25939.062| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.91 r_work: 0.3372 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10081 Z= 0.190 Angle : 0.709 11.751 13683 Z= 0.359 Chirality : 0.045 0.226 1566 Planarity : 0.004 0.040 1727 Dihedral : 6.076 81.211 1398 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.88 % Allowed : 23.16 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1255 helix: 1.27 (0.23), residues: 485 sheet: -0.97 (0.29), residues: 286 loop : -1.08 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 182 TYR 0.022 0.002 TYR D 178 PHE 0.016 0.002 PHE A 336 TRP 0.014 0.002 TRP B 63 HIS 0.006 0.001 HIS R 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10078) covalent geometry : angle 0.70801 / 0.36 (13677) SS BOND : bond 0.01065 / 0.51 ( 3) SS BOND : angle 1.89860 / 0.82 ( 6) hydrogen bonds : bond 0.04387 / 2.97 ( 501) hydrogen bonds : angle 5.24327 / 3.96 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 ASP cc_start: 0.9414 (m-30) cc_final: 0.9175 (m-30) REVERT: R 120 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8563 (mmp) REVERT: R 136 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8216 (t80) REVERT: R 184 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.7891 (tpp-160) REVERT: R 203 MET cc_start: 0.8201 (tpp) cc_final: 0.7805 (tpp) REVERT: R 249 MET cc_start: 0.7371 (mmm) cc_final: 0.7117 (mmm) REVERT: R 316 TRP cc_start: 0.6015 (m100) cc_final: 0.5571 (m100) REVERT: R 346 TYR cc_start: 0.8453 (t80) cc_final: 0.8185 (t80) REVERT: A 21 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7828 (ttm170) REVERT: A 130 LEU cc_start: 0.9331 (mp) cc_final: 0.9088 (mm) REVERT: A 205 ARG cc_start: 0.8885 (mmt90) cc_final: 0.8538 (mmt180) REVERT: A 207 GLU cc_start: 0.8814 (tp30) cc_final: 0.8186 (tm-30) REVERT: A 244 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8094 (m90) REVERT: A 248 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8959 (mttt) REVERT: A 256 ASN cc_start: 0.8890 (t0) cc_final: 0.8384 (t0) REVERT: A 257 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8925 (ttpp) REVERT: A 308 GLU cc_start: 0.7342 (pt0) cc_final: 0.6968 (pt0) REVERT: A 348 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7478 (pp) REVERT: B 105 TYR cc_start: 0.8516 (t80) cc_final: 0.8212 (t80) REVERT: B 142 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7909 (t-170) REVERT: B 148 CYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 226 GLU cc_start: 0.8855 (mp0) cc_final: 0.8217 (mp0) REVERT: B 325 MET cc_start: 0.8872 (mmm) cc_final: 0.8484 (mmm) REVERT: C 14 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8559 (mmtm) REVERT: C 22 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: C 29 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9051 (mmmt) REVERT: C 58 GLU cc_start: 0.9084 (tp30) cc_final: 0.8870 (tp30) REVERT: D 39 GLN cc_start: 0.7424 (tt0) cc_final: 0.6749 (tt0) REVERT: D 46 GLU cc_start: 0.8181 (tt0) cc_final: 0.7605 (pt0) REVERT: D 80 PHE cc_start: 0.7495 (m-80) cc_final: 0.7220 (m-80) REVERT: D 171 GLN cc_start: 0.7712 (mt0) cc_final: 0.7018 (mp-120) REVERT: D 211 ASP cc_start: 0.9009 (t0) cc_final: 0.8274 (t0) REVERT: D 218 MET cc_start: 0.8723 (ttt) cc_final: 0.8266 (ttt) outliers start: 51 outliers final: 35 residues processed: 204 average time/residue: 0.0973 time to fit residues: 26.9864 Evaluate side-chains 209 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 268 ARG Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083995 restraints weight = 26128.255| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.87 r_work: 0.3337 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10081 Z= 0.208 Angle : 0.717 10.647 13683 Z= 0.365 Chirality : 0.046 0.272 1566 Planarity : 0.004 0.037 1727 Dihedral : 6.150 80.470 1398 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 4.88 % Allowed : 22.97 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1255 helix: 1.22 (0.23), residues: 485 sheet: -0.99 (0.29), residues: 290 loop : -1.06 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 166 TYR 0.022 0.002 TYR D 178 PHE 0.015 0.002 PHE A 259 TRP 0.013 0.002 TRP B 63 HIS 0.007 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (10078) covalent geometry : angle 0.71562 / 0.36 (13677) SS BOND : bond 0.01081 / 0.52 ( 3) SS BOND : angle 1.94162 / 0.84 ( 6) hydrogen bonds : bond 0.04403 / 2.96 ( 501) hydrogen bonds : angle 5.27333 / 4.00 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: 0.8938 (tpt) cc_final: 0.8647 (mmt) REVERT: R 136 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8156 (t80) REVERT: R 203 MET cc_start: 0.8271 (tpp) cc_final: 0.7878 (tpp) REVERT: R 249 MET cc_start: 0.7234 (mmm) cc_final: 0.6972 (mmm) REVERT: R 305 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8545 (mp) REVERT: R 343 HIS cc_start: 0.8959 (m90) cc_final: 0.8338 (m170) REVERT: R 346 TYR cc_start: 0.8500 (t80) cc_final: 0.8246 (t80) REVERT: R 363 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8516 (tp) REVERT: A 21 ARG cc_start: 0.8413 (ttp-170) cc_final: 0.7844 (ttm170) REVERT: A 58 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8706 (mm-30) REVERT: A 130 LEU cc_start: 0.9203 (mp) cc_final: 0.8939 (mm) REVERT: A 205 ARG cc_start: 0.8898 (mmt90) cc_final: 0.8541 (mmt180) REVERT: A 207 GLU cc_start: 0.8812 (tp30) cc_final: 0.8172 (tm-30) REVERT: A 244 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8181 (m90) REVERT: A 248 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8964 (mttt) REVERT: A 256 ASN cc_start: 0.8901 (t0) cc_final: 0.8364 (t0) REVERT: A 257 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8902 (ttpp) REVERT: A 308 GLU cc_start: 0.7380 (pt0) cc_final: 0.7000 (pt0) REVERT: A 348 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7649 (pp) REVERT: B 105 TYR cc_start: 0.8497 (t80) cc_final: 0.8117 (t80) REVERT: B 142 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7894 (t-170) REVERT: B 148 CYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7368 (m) REVERT: B 226 GLU cc_start: 0.8943 (mp0) cc_final: 0.8367 (mp0) REVERT: B 262 MET cc_start: 0.8513 (tpp) cc_final: 0.8029 (tpp) REVERT: B 325 MET cc_start: 0.8882 (mmm) cc_final: 0.8515 (mmm) REVERT: C 14 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8497 (mmtm) REVERT: C 22 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: C 29 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9019 (mmmt) REVERT: D 39 GLN cc_start: 0.7428 (tt0) cc_final: 0.6772 (tt0) REVERT: D 46 GLU cc_start: 0.8247 (tt0) cc_final: 0.7647 (pt0) REVERT: D 80 PHE cc_start: 0.7612 (m-80) cc_final: 0.7364 (m-80) REVERT: D 93 MET cc_start: 0.7644 (tpp) cc_final: 0.7372 (tpp) REVERT: D 171 GLN cc_start: 0.7768 (mt0) cc_final: 0.7098 (mp-120) REVERT: D 211 ASP cc_start: 0.9024 (t0) cc_final: 0.8303 (t0) REVERT: D 218 MET cc_start: 0.8755 (ttt) cc_final: 0.8302 (ttt) outliers start: 51 outliers final: 35 residues processed: 205 average time/residue: 0.0886 time to fit residues: 25.2526 Evaluate side-chains 211 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.109017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083408 restraints weight = 26127.056| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.91 r_work: 0.3331 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10081 Z= 0.210 Angle : 0.733 10.780 13683 Z= 0.372 Chirality : 0.046 0.259 1566 Planarity : 0.004 0.038 1727 Dihedral : 6.116 79.662 1395 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 4.59 % Allowed : 23.73 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.24), residues: 1255 helix: 1.13 (0.23), residues: 485 sheet: -1.04 (0.30), residues: 285 loop : -1.01 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 166 TYR 0.022 0.002 TYR D 178 PHE 0.015 0.002 PHE A 336 TRP 0.013 0.002 TRP B 63 HIS 0.005 0.001 HIS R 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (10078) covalent geometry : angle 0.73170 / 0.37 (13677) SS BOND : bond 0.01117 / 0.54 ( 3) SS BOND : angle 1.95894 / 0.86 ( 6) hydrogen bonds : bond 0.04504 / 3.05 ( 501) hydrogen bonds : angle 5.32735 / 4.03 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 ASP cc_start: 0.9499 (m-30) cc_final: 0.9293 (m-30) REVERT: R 120 MET cc_start: 0.8910 (tpt) cc_final: 0.8647 (mmt) REVERT: R 136 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8119 (t80) REVERT: R 203 MET cc_start: 0.8135 (tpp) cc_final: 0.7700 (tpp) REVERT: R 249 MET cc_start: 0.7147 (mmm) cc_final: 0.6878 (mmm) REVERT: R 305 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8552 (mp) REVERT: R 343 HIS cc_start: 0.8829 (m90) cc_final: 0.8254 (m170) REVERT: R 363 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 21 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.7850 (ttm170) REVERT: A 58 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8572 (mm-30) REVERT: A 205 ARG cc_start: 0.8893 (mmt90) cc_final: 0.8521 (mmt180) REVERT: A 207 GLU cc_start: 0.8809 (tp30) cc_final: 0.8580 (tp30) REVERT: A 244 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8140 (m90) REVERT: A 248 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8961 (mttt) REVERT: A 256 ASN cc_start: 0.8916 (t0) cc_final: 0.8367 (t0) REVERT: A 308 GLU cc_start: 0.7385 (pt0) cc_final: 0.7006 (pt0) REVERT: A 348 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7682 (pp) REVERT: B 105 TYR cc_start: 0.8535 (t80) cc_final: 0.8123 (t80) REVERT: B 142 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7836 (t-170) REVERT: B 148 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7355 (m) REVERT: B 226 GLU cc_start: 0.9002 (mp0) cc_final: 0.8502 (mp0) REVERT: B 262 MET cc_start: 0.8541 (tpp) cc_final: 0.8073 (tpp) REVERT: B 325 MET cc_start: 0.8921 (mmm) cc_final: 0.8536 (mmm) REVERT: C 14 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8650 (mmtt) REVERT: C 22 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: C 29 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8968 (mmmm) REVERT: D 39 GLN cc_start: 0.7446 (tt0) cc_final: 0.6939 (tt0) REVERT: D 46 GLU cc_start: 0.8238 (tt0) cc_final: 0.7654 (pt0) REVERT: D 80 PHE cc_start: 0.7691 (m-80) cc_final: 0.7438 (m-80) REVERT: D 93 MET cc_start: 0.7655 (tpp) cc_final: 0.7368 (tpp) REVERT: D 171 GLN cc_start: 0.7821 (mt0) cc_final: 0.7191 (mp-120) REVERT: D 211 ASP cc_start: 0.8959 (t0) cc_final: 0.8271 (t0) REVERT: D 218 MET cc_start: 0.8798 (ttt) cc_final: 0.8347 (ttt) outliers start: 48 outliers final: 32 residues processed: 203 average time/residue: 0.0880 time to fit residues: 24.4954 Evaluate side-chains 204 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 268 ARG Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.110349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.084910 restraints weight = 25714.012| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.86 r_work: 0.3357 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10081 Z= 0.166 Angle : 0.744 17.726 13683 Z= 0.369 Chirality : 0.045 0.316 1566 Planarity : 0.004 0.042 1727 Dihedral : 6.029 78.760 1395 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 4.31 % Allowed : 23.54 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1255 helix: 1.16 (0.23), residues: 485 sheet: -1.05 (0.30), residues: 276 loop : -0.96 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 166 TYR 0.026 0.002 TYR R 346 PHE 0.015 0.002 PHE A 336 TRP 0.012 0.001 TRP B 169 HIS 0.014 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (10078) covalent geometry : angle 0.74373 / 0.37 (13677) SS BOND : bond 0.00952 / 0.46 ( 3) SS BOND : angle 1.73512 / 0.74 ( 6) hydrogen bonds : bond 0.04305 / 2.92 ( 501) hydrogen bonds : angle 5.27645 / 3.98 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 ASP cc_start: 0.9545 (m-30) cc_final: 0.9292 (m-30) REVERT: R 120 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8561 (mmt) REVERT: R 136 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8073 (t80) REVERT: R 174 PHE cc_start: 0.8881 (m-80) cc_final: 0.8271 (m-80) REVERT: R 203 MET cc_start: 0.8097 (tpp) cc_final: 0.7657 (tpp) REVERT: R 249 MET cc_start: 0.6906 (mmm) cc_final: 0.6579 (mmm) REVERT: R 317 LEU cc_start: 0.8461 (tp) cc_final: 0.8212 (tt) REVERT: R 343 HIS cc_start: 0.8839 (m90) cc_final: 0.8279 (m170) REVERT: R 363 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 21 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.7829 (ttm170) REVERT: A 58 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: A 198 MET cc_start: 0.7071 (ttp) cc_final: 0.6739 (ttp) REVERT: A 205 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8512 (mmt180) REVERT: A 244 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8279 (m90) REVERT: A 247 MET cc_start: 0.9201 (mtm) cc_final: 0.8693 (mtm) REVERT: A 256 ASN cc_start: 0.8903 (t0) cc_final: 0.8359 (t0) REVERT: A 257 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8971 (ttpp) REVERT: A 262 THR cc_start: 0.8302 (m) cc_final: 0.8081 (m) REVERT: A 308 GLU cc_start: 0.7340 (pt0) cc_final: 0.7116 (pt0) REVERT: A 310 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 348 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7411 (pp) REVERT: B 105 TYR cc_start: 0.8574 (t80) cc_final: 0.8213 (t80) REVERT: B 142 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7855 (t-170) REVERT: B 148 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7366 (m) REVERT: B 226 GLU cc_start: 0.8985 (mp0) cc_final: 0.8477 (mp0) REVERT: B 234 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: B 262 MET cc_start: 0.8520 (tpp) cc_final: 0.8001 (tpp) REVERT: B 325 MET cc_start: 0.8868 (mmm) cc_final: 0.8461 (mmm) REVERT: C 14 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8615 (mmtm) REVERT: C 22 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: C 29 LYS cc_start: 0.9341 (mmmt) cc_final: 0.8967 (mmmm) REVERT: D 46 GLU cc_start: 0.8249 (tt0) cc_final: 0.7630 (pt0) REVERT: D 80 PHE cc_start: 0.7664 (m-80) cc_final: 0.7169 (m-80) REVERT: D 93 MET cc_start: 0.7624 (tpp) cc_final: 0.7308 (tpp) REVERT: D 171 GLN cc_start: 0.7849 (mt0) cc_final: 0.7191 (mp-120) REVERT: D 211 ASP cc_start: 0.8913 (t0) cc_final: 0.8239 (t0) REVERT: D 218 MET cc_start: 0.8709 (ttt) cc_final: 0.8179 (ttt) outliers start: 45 outliers final: 28 residues processed: 204 average time/residue: 0.1048 time to fit residues: 29.9334 Evaluate side-chains 200 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.111297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085948 restraints weight = 25853.307| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.90 r_work: 0.3371 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10081 Z= 0.154 Angle : 0.718 11.840 13683 Z= 0.359 Chirality : 0.045 0.323 1566 Planarity : 0.004 0.037 1727 Dihedral : 5.946 78.092 1395 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 3.64 % Allowed : 24.31 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1255 helix: 1.20 (0.24), residues: 484 sheet: -0.96 (0.31), residues: 275 loop : -0.93 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 166 TYR 0.019 0.001 TYR D 178 PHE 0.012 0.001 PHE A 259 TRP 0.016 0.002 TRP R 316 HIS 0.007 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10078) covalent geometry : angle 0.71777 / 0.36 (13677) SS BOND : bond 0.00882 / 0.42 ( 3) SS BOND : angle 1.63272 / 0.69 ( 6) hydrogen bonds : bond 0.04118 / 2.79 ( 501) hydrogen bonds : angle 5.18577 / 3.91 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.64 seconds wall clock time: 44 minutes 23.33 seconds (2663.33 seconds total)