Starting phenix.real_space_refine on Sat May 2 22:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.map" model { file = "/net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6w_65707/05_2026/9w6w_65707.cif" } resolution = 3.13 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= -0.003 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5588 2.51 5 N 1504 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8793 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2143 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'8K3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8793 At special positions: 0 Unit cell: (108.56, 114.08, 128.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1639 8.00 N 1504 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 192 " distance=2.04 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 124 " distance=2.03 Simple disulfide: pdb=" SG CYS R 311 " - pdb=" SG CYS R 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 221.5 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 35.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.084A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.666A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.810A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.562A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.647A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.032A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.706A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.634A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.704A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.637A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'R' and resid 40 through 68 removed outlier: 4.093A pdb=" N LEU R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 75 No H-bonds generated for 'chain 'R' and resid 73 through 75' Processing helix chain 'R' and resid 76 through 93 removed outlier: 3.800A pdb=" N VAL R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA R 90 " --> pdb=" O ASP R 86 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 103 removed outlier: 4.337A pdb=" N SER R 103 " --> pdb=" O VAL R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 121 removed outlier: 3.636A pdb=" N CYS R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 142 removed outlier: 3.624A pdb=" N ASN R 131 " --> pdb=" O ALA R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 174 removed outlier: 3.960A pdb=" N TRP R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 209 removed outlier: 3.866A pdb=" N VAL R 202 " --> pdb=" O PRO R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 233 removed outlier: 3.645A pdb=" N VAL R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY R 232 " --> pdb=" O LYS R 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER R 233 " --> pdb=" O PHE R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 282 Processing helix chain 'R' and resid 282 through 297 removed outlier: 3.767A pdb=" N CYS R 297 " --> pdb=" O VAL R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 311 Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 316 through 339 removed outlier: 3.633A pdb=" N LYS R 320 " --> pdb=" O PRO R 316 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE R 332 " --> pdb=" O TYR R 328 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE R 333 " --> pdb=" O SER R 329 " (cutoff:3.500A) Proline residue: R 335 - end of helix removed outlier: 3.987A pdb=" N TYR R 338 " --> pdb=" O ASN R 334 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR R 339 " --> pdb=" O PRO R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.584A pdb=" N ASN R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.156A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.122A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.794A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.867A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.642A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.660A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.853A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.601A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.572A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.550A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.234A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR E 227 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1041 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: 1.00 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1432 1.29 - 1.42: 2419 1.42 - 1.55: 5041 1.55 - 1.68: 1 1.68 - 1.81: 88 Bond restraints: 8981 Sorted by residual: bond pdb=" C05 8K3 R 401 " pdb=" N06 8K3 R 401 " ideal model delta sigma weight residual 1.371 1.243 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C13 8K3 R 401 " pdb=" N15 8K3 R 401 " ideal model delta sigma weight residual 1.346 1.443 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA PHE R 302 " pdb=" CB PHE R 302 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.56e-02 4.11e+03 2.22e+01 bond pdb=" C SER B 72 " pdb=" O SER B 72 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.22e-02 6.72e+03 1.92e+01 bond pdb=" C ALA B 73 " pdb=" O ALA B 73 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.14e-02 7.69e+03 1.90e+01 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11859 2.25 - 4.50: 273 4.50 - 6.75: 26 6.75 - 9.00: 8 9.00 - 11.25: 2 Bond angle restraints: 12168 Sorted by residual: angle pdb=" C THR R 304 " pdb=" CA THR R 304 " pdb=" CB THR R 304 " ideal model delta sigma weight residual 110.79 102.50 8.29 1.66e+00 3.63e-01 2.50e+01 angle pdb=" CA SER B 72 " pdb=" C SER B 72 " pdb=" O SER B 72 " ideal model delta sigma weight residual 121.06 115.85 5.21 1.16e+00 7.43e-01 2.02e+01 angle pdb=" N PHE R 302 " pdb=" CA PHE R 302 " pdb=" C PHE R 302 " ideal model delta sigma weight residual 111.28 115.98 -4.70 1.09e+00 8.42e-01 1.86e+01 angle pdb=" N VAL B 71 " pdb=" CA VAL B 71 " pdb=" CB VAL B 71 " ideal model delta sigma weight residual 111.44 118.20 -6.76 1.64e+00 3.72e-01 1.70e+01 angle pdb=" CA THR R 133 " pdb=" CB THR R 133 " pdb=" OG1 THR R 133 " ideal model delta sigma weight residual 109.60 103.89 5.71 1.50e+00 4.44e-01 1.45e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4469 17.29 - 34.58: 604 34.58 - 51.87: 194 51.87 - 69.16: 35 69.16 - 86.45: 11 Dihedral angle restraints: 5313 sinusoidal: 2051 harmonic: 3262 Sorted by residual: dihedral pdb=" CB CYS R 311 " pdb=" SG CYS R 311 " pdb=" SG CYS R 313 " pdb=" CB CYS R 313 " ideal model delta sinusoidal sigma weight residual -86.00 -159.76 73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS R 120 " pdb=" SG CYS R 120 " pdb=" SG CYS R 124 " pdb=" CB CYS R 124 " ideal model delta sinusoidal sigma weight residual -86.00 -138.00 52.00 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1267 0.103 - 0.206: 93 0.206 - 0.310: 5 0.310 - 0.413: 1 0.413 - 0.516: 2 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CG LEU R 151 " pdb=" CB LEU R 151 " pdb=" CD1 LEU R 151 " pdb=" CD2 LEU R 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA PHE R 302 " pdb=" N PHE R 302 " pdb=" C PHE R 302 " pdb=" CB PHE R 302 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1365 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 243 " 0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C THR B 243 " -0.089 2.00e-02 2.50e+03 pdb=" O THR B 243 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY B 244 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 305 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLU R 305 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU R 305 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU R 306 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 258 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" CG ASP B 258 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP B 258 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 258 " 0.013 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 754 2.74 - 3.28: 8097 3.28 - 3.82: 13552 3.82 - 4.36: 15736 4.36 - 4.90: 28693 Nonbonded interactions: 66832 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.284 3.040 nonbonded pdb=" O THR R 54 " pdb=" ND2 ASN R 58 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLN E 142 " pdb=" OG1 THR E 243 " model vdw 2.301 3.040 ... (remaining 66827 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: 0.960 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 8984 Z= 0.383 Angle : 0.741 11.254 12174 Z= 0.470 Chirality : 0.054 0.516 1368 Planarity : 0.004 0.060 1540 Dihedral : 17.749 86.451 3198 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.43 % Allowed : 26.56 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.37 (0.26), residues: 1110 helix: 0.75 (0.30), residues: 362 sheet: 0.50 (0.31), residues: 269 loop : -1.47 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.011 0.001 TYR B 264 PHE 0.019 0.001 PHE R 301 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 100 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 8981) covalent geometry : angle 0.73997 (12168) SS BOND : bond 0.00465 ( 3) SS BOND : angle 1.85546 ( 6) hydrogen bonds : bond 0.20558 ( 365) hydrogen bonds : angle 7.06054 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.295 Fit side-chains REVERT: B 17 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 242 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8060 (mmm-85) REVERT: R 82 MET cc_start: 0.7382 (tmm) cc_final: 0.7057 (ttt) REVERT: R 106 ARG cc_start: 0.7094 (tmt170) cc_final: 0.6709 (ttp80) REVERT: R 149 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7191 (t80) REVERT: R 152 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7129 (mtm-85) outliers start: 23 outliers final: 4 residues processed: 150 average time/residue: 0.1174 time to fit residues: 22.8267 Evaluate side-chains 136 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 156 CYS Chi-restraints excluded: chain R residue 158 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 259 GLN R 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.174203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112793 restraints weight = 10780.583| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.86 r_work: 0.3108 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8984 Z= 0.129 Angle : 0.532 7.487 12174 Z= 0.280 Chirality : 0.042 0.147 1368 Planarity : 0.003 0.031 1540 Dihedral : 5.484 76.071 1230 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.49 % Allowed : 24.87 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.02 (0.25), residues: 1110 helix: 1.30 (0.29), residues: 365 sheet: 0.74 (0.31), residues: 269 loop : -1.49 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.013 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8981) covalent geometry : angle 0.52780 (12168) SS BOND : bond 0.00556 ( 3) SS BOND : angle 3.04708 ( 6) hydrogen bonds : bond 0.04666 ( 365) hydrogen bonds : angle 4.61920 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8364 (ttm110) REVERT: B 260 GLU cc_start: 0.8187 (tt0) cc_final: 0.7937 (tt0) REVERT: C 32 LYS cc_start: 0.8130 (tptm) cc_final: 0.7752 (tptp) REVERT: C 58 GLU cc_start: 0.8468 (pm20) cc_final: 0.8185 (pm20) REVERT: A 242 ARG cc_start: 0.8301 (mtt180) cc_final: 0.8063 (mmm-85) REVERT: R 149 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7905 (t80) REVERT: R 152 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7395 (mtm-85) REVERT: R 334 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6709 (t0) outliers start: 33 outliers final: 13 residues processed: 160 average time/residue: 0.1333 time to fit residues: 27.5691 Evaluate side-chains 149 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 334 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3980 r_free = 0.3980 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112958 restraints weight = 10718.273| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.86 r_work: 0.3130 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8984 Z= 0.116 Angle : 0.495 6.107 12174 Z= 0.263 Chirality : 0.041 0.131 1368 Planarity : 0.003 0.025 1540 Dihedral : 5.183 76.085 1225 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.43 % Allowed : 25.82 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.17 (0.25), residues: 1110 helix: 1.47 (0.29), residues: 366 sheet: 0.96 (0.31), residues: 259 loop : -1.50 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.013 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 100 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8981) covalent geometry : angle 0.49333 (12168) SS BOND : bond 0.00369 ( 3) SS BOND : angle 1.98574 ( 6) hydrogen bonds : bond 0.04167 ( 365) hydrogen bonds : angle 4.26264 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: B 260 GLU cc_start: 0.8197 (tt0) cc_final: 0.7876 (tt0) REVERT: C 32 LYS cc_start: 0.8112 (tptm) cc_final: 0.7744 (tptp) REVERT: C 58 GLU cc_start: 0.8485 (pm20) cc_final: 0.8183 (pm20) REVERT: A 242 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8036 (mmm-85) REVERT: R 69 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5464 (mmm160) REVERT: R 82 MET cc_start: 0.7446 (tmm) cc_final: 0.7222 (ttp) REVERT: R 152 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7362 (mtm-85) REVERT: R 334 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6112 (t0) outliers start: 23 outliers final: 11 residues processed: 154 average time/residue: 0.1264 time to fit residues: 25.5065 Evaluate side-chains 144 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 334 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112902 restraints weight = 10872.575| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.88 r_work: 0.3126 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8984 Z= 0.118 Angle : 0.501 6.973 12174 Z= 0.265 Chirality : 0.041 0.154 1368 Planarity : 0.003 0.038 1540 Dihedral : 5.036 77.197 1223 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.86 % Allowed : 27.30 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.25 (0.25), residues: 1110 helix: 1.59 (0.29), residues: 365 sheet: 1.02 (0.31), residues: 259 loop : -1.49 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.012 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8981) covalent geometry : angle 0.49951 (12168) SS BOND : bond 0.00247 ( 3) SS BOND : angle 2.00079 ( 6) hydrogen bonds : bond 0.04017 ( 365) hydrogen bonds : angle 4.12104 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.364 Fit side-chains REVERT: B 234 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 260 GLU cc_start: 0.8215 (tt0) cc_final: 0.7876 (tt0) REVERT: C 32 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7762 (tptp) REVERT: C 58 GLU cc_start: 0.8499 (pm20) cc_final: 0.8188 (pm20) REVERT: A 197 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: R 69 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5446 (mmm160) REVERT: R 152 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7371 (mtm-85) REVERT: R 334 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6114 (t0) outliers start: 27 outliers final: 15 residues processed: 146 average time/residue: 0.1353 time to fit residues: 25.5043 Evaluate side-chains 143 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 334 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.0470 chunk 104 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114467 restraints weight = 10781.623| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.86 r_work: 0.3134 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8984 Z= 0.098 Angle : 0.481 7.762 12174 Z= 0.252 Chirality : 0.041 0.130 1368 Planarity : 0.003 0.042 1540 Dihedral : 4.899 76.520 1223 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.96 % Allowed : 26.98 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.36 (0.25), residues: 1110 helix: 1.65 (0.29), residues: 367 sheet: 1.08 (0.30), residues: 265 loop : -1.45 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.012 0.001 TYR E 190 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8981) covalent geometry : angle 0.47943 (12168) SS BOND : bond 0.00223 ( 3) SS BOND : angle 1.67663 ( 6) hydrogen bonds : bond 0.03570 ( 365) hydrogen bonds : angle 3.94962 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.353 Fit side-chains REVERT: B 234 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: C 32 LYS cc_start: 0.8035 (tptm) cc_final: 0.7658 (tptp) REVERT: C 58 GLU cc_start: 0.8487 (pm20) cc_final: 0.8170 (pm20) REVERT: A 188 HIS cc_start: 0.8414 (m90) cc_final: 0.7841 (m-70) REVERT: A 197 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8035 (mtpp) REVERT: E 166 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6281 (tt) REVERT: R 69 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5462 (mmm160) REVERT: R 149 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: R 152 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7342 (mtm-85) outliers start: 28 outliers final: 13 residues processed: 157 average time/residue: 0.1266 time to fit residues: 26.0540 Evaluate side-chains 150 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 99 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 47 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 334 ASN 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 = 0.174734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113472 restraints weight = 10788.234| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.87 r_work: 0.3118 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8984 Z= 0.113 Angle : 0.497 6.391 12174 Z= 0.261 Chirality : 0.041 0.143 1368 Planarity : 0.003 0.045 1540 Dihedral : 4.960 77.027 1223 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.86 % Allowed : 27.62 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.25), residues: 1110 helix: 1.68 (0.29), residues: 366 sheet: 1.11 (0.31), residues: 268 loop : -1.40 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.012 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8981) covalent geometry : angle 0.49592 (12168) SS BOND : bond 0.00263 ( 3) SS BOND : angle 1.83404 ( 6) hydrogen bonds : bond 0.03822 ( 365) hydrogen bonds : angle 3.90764 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 19 ARG cc_start: 0.8508 (ptm-80) cc_final: 0.8246 (ptm-80) REVERT: B 234 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: B 260 GLU cc_start: 0.8287 (tt0) cc_final: 0.7977 (tt0) REVERT: C 32 LYS cc_start: 0.8129 (tptm) cc_final: 0.7742 (tptp) REVERT: C 58 GLU cc_start: 0.8520 (pm20) cc_final: 0.8165 (pm20) REVERT: E 166 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6312 (tt) REVERT: R 69 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.5467 (mmm160) REVERT: R 149 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: R 152 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7295 (mtm-85) outliers start: 27 outliers final: 15 residues processed: 155 average time/residue: 0.1256 time to fit residues: 25.5556 Evaluate side-chains 149 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112911 restraints weight = 10698.835| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.73 r_work: 0.3136 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8984 Z= 0.129 Angle : 0.518 9.038 12174 Z= 0.271 Chirality : 0.042 0.132 1368 Planarity : 0.003 0.049 1540 Dihedral : 5.032 76.902 1223 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.07 % Allowed : 26.88 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.44 (0.25), residues: 1110 helix: 1.70 (0.29), residues: 363 sheet: 1.11 (0.31), residues: 266 loop : -1.35 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.012 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8981) covalent geometry : angle 0.51691 (12168) SS BOND : bond 0.00313 ( 3) SS BOND : angle 1.78354 ( 6) hydrogen bonds : bond 0.04126 ( 365) hydrogen bonds : angle 3.92648 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.334 Fit side-chains REVERT: B 234 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: C 32 LYS cc_start: 0.8083 (tptm) cc_final: 0.7799 (tptp) REVERT: C 58 GLU cc_start: 0.8564 (pm20) cc_final: 0.8193 (pm20) REVERT: A 188 HIS cc_start: 0.8388 (m90) cc_final: 0.7995 (m-70) REVERT: A 197 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8251 (mtpp) REVERT: E 166 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6424 (tt) REVERT: R 69 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5521 (mmm160) REVERT: R 149 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: R 152 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7260 (mtm-85) outliers start: 29 outliers final: 16 residues processed: 157 average time/residue: 0.1258 time to fit residues: 26.1048 Evaluate side-chains 157 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109350 restraints weight = 10768.366| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.84 r_work: 0.3071 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8984 Z= 0.200 Angle : 0.585 8.098 12174 Z= 0.307 Chirality : 0.044 0.139 1368 Planarity : 0.004 0.051 1540 Dihedral : 5.460 80.140 1223 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.75 % Allowed : 27.94 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.31 (0.25), residues: 1110 helix: 1.53 (0.29), residues: 363 sheet: 1.04 (0.31), residues: 265 loop : -1.37 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.015 0.002 TYR R 220 PHE 0.016 0.002 PHE B 241 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8981) covalent geometry : angle 0.58364 (12168) SS BOND : bond 0.00517 ( 3) SS BOND : angle 2.13503 ( 6) hydrogen bonds : bond 0.05260 ( 365) hydrogen bonds : angle 4.14713 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.284 Fit side-chains REVERT: B 234 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 260 GLU cc_start: 0.8338 (tt0) cc_final: 0.7992 (tt0) REVERT: B 273 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9053 (mp) REVERT: C 32 LYS cc_start: 0.8078 (tptm) cc_final: 0.7814 (tptp) REVERT: C 58 GLU cc_start: 0.8593 (pm20) cc_final: 0.8176 (pm20) REVERT: A 197 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8021 (mtpp) REVERT: E 166 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6372 (tt) REVERT: R 152 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7226 (mtm-85) outliers start: 26 outliers final: 18 residues processed: 155 average time/residue: 0.1246 time to fit residues: 25.1890 Evaluate side-chains 153 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3977 r_free = 0.3977 target = 0.174124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113195 restraints weight = 10608.022| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.86 r_work: 0.3130 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8984 Z= 0.105 Angle : 0.516 6.948 12174 Z= 0.269 Chirality : 0.041 0.130 1368 Planarity : 0.003 0.057 1540 Dihedral : 5.061 76.991 1223 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.54 % Allowed : 28.36 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.42 (0.25), residues: 1110 helix: 1.64 (0.29), residues: 363 sheet: 1.14 (0.31), residues: 265 loop : -1.34 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.011 0.001 TYR E 190 PHE 0.013 0.001 PHE B 241 TRP 0.015 0.001 TRP R 325 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8981) covalent geometry : angle 0.51465 (12168) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.91480 ( 6) hydrogen bonds : bond 0.03707 ( 365) hydrogen bonds : angle 3.91696 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.365 Fit side-chains REVERT: B 234 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 273 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9043 (mp) REVERT: C 32 LYS cc_start: 0.8014 (tptm) cc_final: 0.7739 (tptp) REVERT: C 58 GLU cc_start: 0.8524 (pm20) cc_final: 0.8189 (pm20) REVERT: E 166 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6364 (tt) REVERT: R 106 ARG cc_start: 0.7219 (tmt170) cc_final: 0.6832 (ttp80) REVERT: R 149 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: R 152 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7221 (mtm-85) outliers start: 24 outliers final: 16 residues processed: 155 average time/residue: 0.1253 time to fit residues: 25.3568 Evaluate side-chains 158 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3950 r_free = 0.3950 target = 0.171507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110044 restraints weight = 10676.000| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.84 r_work: 0.3085 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8984 Z= 0.182 Angle : 0.579 7.705 12174 Z= 0.303 Chirality : 0.044 0.137 1368 Planarity : 0.004 0.085 1540 Dihedral : 5.339 80.494 1223 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.12 % Allowed : 28.78 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.31 (0.25), residues: 1110 helix: 1.52 (0.29), residues: 363 sheet: 1.07 (0.31), residues: 265 loop : -1.37 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 214 TYR 0.014 0.001 TYR R 220 PHE 0.015 0.002 PHE B 241 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8981) covalent geometry : angle 0.57718 (12168) SS BOND : bond 0.00454 ( 3) SS BOND : angle 2.09374 ( 6) hydrogen bonds : bond 0.04961 ( 365) hydrogen bonds : angle 4.07755 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.337 Fit side-chains REVERT: B 234 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 260 GLU cc_start: 0.8349 (tt0) cc_final: 0.7997 (tt0) REVERT: B 273 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9063 (mp) REVERT: C 32 LYS cc_start: 0.8023 (tptm) cc_final: 0.7750 (tptp) REVERT: C 58 GLU cc_start: 0.8583 (pm20) cc_final: 0.8181 (pm20) REVERT: E 166 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6446 (tt) REVERT: R 106 ARG cc_start: 0.7125 (tmt170) cc_final: 0.6653 (ttp80) REVERT: R 152 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7243 (mtm-85) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.1321 time to fit residues: 25.2979 Evaluate side-chains 151 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109884 restraints weight = 10624.030| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.83 r_work: 0.3067 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8984 Z= 0.190 Angle : 0.594 7.627 12174 Z= 0.310 Chirality : 0.044 0.135 1368 Planarity : 0.004 0.071 1540 Dihedral : 5.454 82.550 1223 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.75 % Allowed : 28.47 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.22 (0.25), residues: 1110 helix: 1.42 (0.28), residues: 363 sheet: 1.01 (0.31), residues: 265 loop : -1.39 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 214 TYR 0.013 0.001 TYR R 220 PHE 0.015 0.002 PHE B 241 TRP 0.024 0.002 TRP R 325 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8981) covalent geometry : angle 0.59241 (12168) SS BOND : bond 0.00475 ( 3) SS BOND : angle 2.05990 ( 6) hydrogen bonds : bond 0.05063 ( 365) hydrogen bonds : angle 4.14119 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.41 seconds wall clock time: 52 minutes 48.86 seconds (3168.86 seconds total)