Starting phenix.real_space_refine on Wed Mar 4 04:00:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgy_31980/03_2026/7vgy_31980.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2128 atoms to isotropic. 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 I 1 10.91 5 S 61 5.16 5 C 5603 2.51 5 N 1468 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2201 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: "D" 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: "E" 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'ML2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.21, per 1000 atoms: 0.25 Number of scatterers: 8748 At special positions: 0 Unit cell: (94.62, 118.69, 123.67, 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) I 1 52.95 S 61 16.00 O 1615 8.00 N 1468 7.00 C 5603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 332.2 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 37.8% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 23 through 55 Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.832A pdb=" N ILE A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.095A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 130 removed outlier: 3.886A pdb=" N CYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.852A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.630A pdb=" N THR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.919A pdb=" N ILE A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.548A pdb=" N TRP A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.755A pdb=" N ILE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.597A pdb=" N MET A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 297 removed outlier: 3.823A pdb=" N ALA A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.750A pdb=" N GLU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.918A pdb=" N ARG B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.675A pdb=" N ILE B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.010A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 242 through 255 Processing helix chain 'B' and resid 270 through 278 removed outlier: 4.013A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.980A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.978A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.743A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.568A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.683A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.269A pdb=" N VAL B 33 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE B 199 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 35 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.773A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.618A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.711A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.573A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.579A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.691A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.792A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.506A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.506A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.542A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1176 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: 1.45 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2842 1.36 - 1.55: 6007 1.55 - 1.74: 1 1.74 - 1.92: 87 1.92 - 2.11: 1 Bond restraints: 8938 Sorted by residual: bond pdb=" N ILE A 189 " pdb=" CA ILE A 189 " ideal model delta sigma weight residual 1.461 1.384 0.077 1.17e-02 7.31e+03 4.35e+01 bond pdb=" CA TYR A 281 " pdb=" C TYR A 281 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.41e-02 5.03e+03 3.18e+01 bond pdb=" C16 ML2 A 402 " pdb=" N15 ML2 A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CA ILE A 189 " pdb=" CB ILE A 189 " ideal model delta sigma weight residual 1.540 1.481 0.058 1.17e-02 7.31e+03 2.49e+01 bond pdb=" C TYR A 281 " pdb=" O TYR A 281 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.28e-02 6.10e+03 2.03e+01 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11890 1.97 - 3.94: 197 3.94 - 5.90: 40 5.90 - 7.87: 4 7.87 - 9.84: 3 Bond angle restraints: 12134 Sorted by residual: angle pdb=" N TYR A 187 " pdb=" CA TYR A 187 " pdb=" C TYR A 187 " ideal model delta sigma weight residual 111.36 101.52 9.84 1.09e+00 8.42e-01 8.15e+01 angle pdb=" N ALA A 186 " pdb=" CA ALA A 186 " pdb=" C ALA A 186 " ideal model delta sigma weight residual 113.01 121.35 -8.34 1.20e+00 6.94e-01 4.83e+01 angle pdb=" N SER A 185 " pdb=" CA SER A 185 " pdb=" C SER A 185 " ideal model delta sigma weight residual 111.71 104.10 7.61 1.15e+00 7.56e-01 4.38e+01 angle pdb=" N ILE A 189 " pdb=" CA ILE A 189 " pdb=" C ILE A 189 " ideal model delta sigma weight residual 110.42 104.95 5.47 9.60e-01 1.09e+00 3.25e+01 angle pdb=" CA CYS C 121 " pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " ideal model delta sigma weight residual 114.40 123.65 -9.25 2.30e+00 1.89e-01 1.62e+01 ... (remaining 12129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4781 17.43 - 34.87: 429 34.87 - 52.30: 80 52.30 - 69.73: 14 69.73 - 87.17: 11 Dihedral angle restraints: 5315 sinusoidal: 2058 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 157.89 -64.89 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -125.51 39.51 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA CYS A 127 " pdb=" C CYS A 127 " pdb=" N TYR A 128 " pdb=" CA TYR A 128 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1308 0.093 - 0.185: 70 0.185 - 0.278: 5 0.278 - 0.371: 0 0.371 - 0.463: 2 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CA ALA A 186 " pdb=" N ALA A 186 " pdb=" C ALA A 186 " pdb=" CB ALA A 186 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA THR A 188 " pdb=" N THR A 188 " pdb=" C THR A 188 " pdb=" CB THR A 188 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA TYR A 281 " pdb=" N TYR A 281 " pdb=" C TYR A 281 " pdb=" CB TYR A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1382 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 279 " 0.027 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C ALA A 279 " -0.096 2.00e-02 2.50e+03 pdb=" O ALA A 279 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 280 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 186 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C ALA A 186 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA A 186 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 187 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 188 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C THR A 188 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 188 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 189 " 0.010 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.75: 939 2.75 - 3.30: 8966 3.30 - 3.85: 15088 3.85 - 4.41: 18860 4.41 - 4.96: 32565 Nonbonded interactions: 76418 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.194 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG E 180 " pdb=" O GLU E 222 " model vdw 2.239 3.120 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.243 3.040 nonbonded pdb=" O GLU B 275 " pdb=" NZ LYS B 279 " model vdw 2.263 3.120 ... (remaining 76413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8941 Z= 0.292 Angle : 0.664 9.840 12140 Z= 0.381 Chirality : 0.048 0.463 1385 Planarity : 0.004 0.055 1524 Dihedral : 14.176 87.168 3208 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.43 % Allowed : 0.53 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.74 (0.26), residues: 1103 helix: 0.10 (0.30), residues: 360 sheet: 0.20 (0.31), residues: 302 loop : -1.41 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 256 TYR 0.019 0.001 TYR A 281 PHE 0.023 0.001 PHE B 274 TRP 0.017 0.001 TRP A 251 HIS 0.003 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8938) covalent geometry : angle 0.66377 (12134) SS BOND : bond 0.00964 ( 3) SS BOND : angle 1.33440 ( 6) hydrogen bonds : bond 0.15656 ( 401) hydrogen bonds : angle 7.20884 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 0.338 Fit side-chains REVERT: A 34 LEU cc_start: 0.6761 (tp) cc_final: 0.6551 (tt) REVERT: A 36 PHE cc_start: 0.7632 (t80) cc_final: 0.6786 (m-10) REVERT: A 117 ASN cc_start: 0.8550 (m110) cc_final: 0.8281 (m110) REVERT: A 134 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7793 (mttt) REVERT: B 20 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6776 (ttp80) outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 0.1152 time to fit residues: 28.1485 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 188 HIS E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112619 restraints weight = 12150.179| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.76 r_work: 0.3400 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8941 Z= 0.173 Angle : 0.610 9.591 12140 Z= 0.321 Chirality : 0.043 0.152 1385 Planarity : 0.004 0.047 1524 Dihedral : 5.554 50.500 1285 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.82 % Allowed : 9.83 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.55 (0.26), residues: 1103 helix: 0.44 (0.29), residues: 360 sheet: 0.28 (0.31), residues: 289 loop : -1.43 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.016 0.001 TYR B 302 PHE 0.018 0.002 PHE B 274 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8938) covalent geometry : angle 0.60918 (12134) SS BOND : bond 0.00978 ( 3) SS BOND : angle 1.47291 ( 6) hydrogen bonds : bond 0.03992 ( 401) hydrogen bonds : angle 4.96943 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7953 (t80) cc_final: 0.6736 (m-10) REVERT: A 117 ASN cc_start: 0.8792 (m110) cc_final: 0.8499 (m-40) REVERT: A 134 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7752 (mttt) REVERT: A 146 CYS cc_start: 0.7738 (p) cc_final: 0.7475 (p) REVERT: A 219 GLN cc_start: 0.7752 (tp40) cc_final: 0.7525 (tp40) REVERT: A 268 MET cc_start: 0.4684 (ttm) cc_final: 0.3965 (tpp) REVERT: D 21 MET cc_start: 0.7217 (ptt) cc_final: 0.6976 (ptm) outliers start: 17 outliers final: 13 residues processed: 183 average time/residue: 0.1164 time to fit residues: 27.9957 Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 164 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 0.0040 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 75 GLN C 88 ASN C 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113380 restraints weight = 12600.684| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.79 r_work: 0.3408 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.128 Angle : 0.559 8.316 12140 Z= 0.296 Chirality : 0.041 0.140 1385 Planarity : 0.004 0.047 1524 Dihedral : 5.140 31.660 1283 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.46 % Allowed : 11.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.46 (0.26), residues: 1103 helix: 0.60 (0.29), residues: 360 sheet: 0.27 (0.31), residues: 289 loop : -1.41 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.014 0.001 TYR B 302 PHE 0.013 0.001 PHE B 274 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8938) covalent geometry : angle 0.55860 (12134) SS BOND : bond 0.00803 ( 3) SS BOND : angle 1.22744 ( 6) hydrogen bonds : bond 0.03564 ( 401) hydrogen bonds : angle 4.69032 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7962 (t80) cc_final: 0.6702 (m-10) REVERT: A 117 ASN cc_start: 0.8797 (m110) cc_final: 0.8491 (m-40) REVERT: A 134 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7856 (mtpt) REVERT: A 146 CYS cc_start: 0.7743 (p) cc_final: 0.7474 (p) REVERT: A 219 GLN cc_start: 0.7740 (tp40) cc_final: 0.7519 (tp40) REVERT: A 268 MET cc_start: 0.4088 (ttm) cc_final: 0.3624 (tpp) REVERT: A 281 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.4627 (t80) REVERT: B 31 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8487 (mtt90) REVERT: B 315 ASP cc_start: 0.8084 (p0) cc_final: 0.7857 (p0) REVERT: D 21 MET cc_start: 0.7172 (ptt) cc_final: 0.6938 (ptm) REVERT: D 42 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8364 (mm-30) REVERT: E 189 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8572 (mt) outliers start: 23 outliers final: 13 residues processed: 182 average time/residue: 0.1141 time to fit residues: 27.3316 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN C 75 GLN C 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112702 restraints weight = 12138.443| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.73 r_work: 0.3401 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.148 Angle : 0.564 8.526 12140 Z= 0.298 Chirality : 0.042 0.153 1385 Planarity : 0.004 0.044 1524 Dihedral : 5.048 30.526 1282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.99 % Allowed : 14.42 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1103 helix: 0.73 (0.29), residues: 361 sheet: 0.20 (0.31), residues: 289 loop : -1.42 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.019 0.001 TYR B 302 PHE 0.016 0.001 PHE A 105 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8938) covalent geometry : angle 0.56364 (12134) SS BOND : bond 0.00895 ( 3) SS BOND : angle 1.18559 ( 6) hydrogen bonds : bond 0.03520 ( 401) hydrogen bonds : angle 4.57084 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7969 (t80) cc_final: 0.6658 (m-10) REVERT: A 101 GLN cc_start: 0.6295 (mm-40) cc_final: 0.5931 (mm-40) REVERT: A 117 ASN cc_start: 0.8791 (m110) cc_final: 0.8474 (m-40) REVERT: A 134 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7929 (mtpt) REVERT: A 146 CYS cc_start: 0.7695 (p) cc_final: 0.7417 (p) REVERT: A 219 GLN cc_start: 0.7708 (tp40) cc_final: 0.7504 (tp40) REVERT: A 268 MET cc_start: 0.4222 (ttm) cc_final: 0.3615 (tpp) REVERT: A 281 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.4606 (t80) REVERT: B 31 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8442 (mtt90) REVERT: C 17 GLN cc_start: 0.7263 (tm-30) cc_final: 0.7053 (tp40) REVERT: D 21 MET cc_start: 0.7178 (ptt) cc_final: 0.6959 (ptm) REVERT: E 189 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8594 (mt) outliers start: 28 outliers final: 18 residues processed: 181 average time/residue: 0.1084 time to fit residues: 25.9606 Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110579 restraints weight = 12192.221| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.75 r_work: 0.3370 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8941 Z= 0.209 Angle : 0.603 9.272 12140 Z= 0.319 Chirality : 0.043 0.174 1385 Planarity : 0.004 0.041 1524 Dihedral : 5.195 30.551 1282 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.06 % Allowed : 14.96 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.51 (0.26), residues: 1103 helix: 0.69 (0.29), residues: 361 sheet: 0.08 (0.31), residues: 291 loop : -1.44 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.020 0.002 TYR B 302 PHE 0.016 0.002 PHE A 179 TRP 0.017 0.001 TRP E 47 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8938) covalent geometry : angle 0.60248 (12134) SS BOND : bond 0.01116 ( 3) SS BOND : angle 1.21660 ( 6) hydrogen bonds : bond 0.03788 ( 401) hydrogen bonds : angle 4.66115 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7965 (t80) cc_final: 0.6627 (m-10) REVERT: A 101 GLN cc_start: 0.6323 (mm-40) cc_final: 0.5914 (mm-40) REVERT: A 117 ASN cc_start: 0.8827 (m110) cc_final: 0.8500 (m-40) REVERT: A 134 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7934 (mtpt) REVERT: A 146 CYS cc_start: 0.7725 (p) cc_final: 0.7438 (p) REVERT: A 219 GLN cc_start: 0.7727 (tp40) cc_final: 0.7504 (tp40) REVERT: A 268 MET cc_start: 0.4418 (ttm) cc_final: 0.3750 (tpp) REVERT: A 281 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.4612 (t80) REVERT: B 285 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6996 (mp) REVERT: D 21 MET cc_start: 0.7208 (ptt) cc_final: 0.6974 (ptm) REVERT: E 189 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8652 (mt) outliers start: 38 outliers final: 28 residues processed: 189 average time/residue: 0.1074 time to fit residues: 26.7836 Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 93 optimal weight: 0.0060 chunk 88 optimal weight: 0.0170 overall best weight: 0.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115039 restraints weight = 12066.361| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.75 r_work: 0.3435 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8941 Z= 0.105 Angle : 0.536 7.389 12140 Z= 0.283 Chirality : 0.040 0.141 1385 Planarity : 0.003 0.043 1524 Dihedral : 4.889 28.952 1282 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.42 % Allowed : 15.92 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.26 (0.26), residues: 1103 helix: 0.93 (0.29), residues: 364 sheet: 0.12 (0.31), residues: 297 loop : -1.28 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.017 0.001 TYR B 302 PHE 0.012 0.001 PHE A 105 TRP 0.014 0.001 TRP C 82 HIS 0.015 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8938) covalent geometry : angle 0.53524 (12134) SS BOND : bond 0.00581 ( 3) SS BOND : angle 1.00569 ( 6) hydrogen bonds : bond 0.03053 ( 401) hydrogen bonds : angle 4.36037 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7954 (t80) cc_final: 0.6668 (m-10) REVERT: A 101 GLN cc_start: 0.6256 (mm-40) cc_final: 0.5796 (mm-40) REVERT: A 117 ASN cc_start: 0.8811 (m110) cc_final: 0.8482 (m-40) REVERT: A 134 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7994 (mtpt) REVERT: A 146 CYS cc_start: 0.7659 (p) cc_final: 0.7313 (p) REVERT: A 219 GLN cc_start: 0.7633 (tp40) cc_final: 0.7431 (tp40) REVERT: A 268 MET cc_start: 0.4048 (ttm) cc_final: 0.3528 (tpp) REVERT: C 17 GLN cc_start: 0.7300 (tm-30) cc_final: 0.7069 (tp40) REVERT: D 21 MET cc_start: 0.7141 (ptt) cc_final: 0.6932 (ptm) REVERT: E 189 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (mt) outliers start: 32 outliers final: 25 residues processed: 188 average time/residue: 0.1164 time to fit residues: 28.8261 Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113333 restraints weight = 12812.294| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.82 r_work: 0.3406 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.130 Angle : 0.559 7.833 12140 Z= 0.294 Chirality : 0.042 0.184 1385 Planarity : 0.004 0.042 1524 Dihedral : 4.858 28.360 1282 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.42 % Allowed : 17.41 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.28 (0.26), residues: 1103 helix: 0.92 (0.29), residues: 367 sheet: 0.04 (0.31), residues: 299 loop : -1.25 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.019 0.001 TYR B 302 PHE 0.011 0.001 PHE A 179 TRP 0.011 0.001 TRP E 47 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8938) covalent geometry : angle 0.55849 (12134) SS BOND : bond 0.00783 ( 3) SS BOND : angle 1.04383 ( 6) hydrogen bonds : bond 0.03223 ( 401) hydrogen bonds : angle 4.37981 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 36 PHE cc_start: 0.7961 (t80) cc_final: 0.6663 (m-10) REVERT: A 101 GLN cc_start: 0.6263 (mm-40) cc_final: 0.5834 (mm-40) REVERT: A 117 ASN cc_start: 0.8828 (m110) cc_final: 0.8506 (m-40) REVERT: A 134 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7979 (mtpt) REVERT: A 219 GLN cc_start: 0.7683 (tp40) cc_final: 0.7409 (tp40) REVERT: A 268 MET cc_start: 0.4012 (ttm) cc_final: 0.3488 (tpp) REVERT: A 281 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.4750 (t80) REVERT: B 31 ARG cc_start: 0.8683 (mtt90) cc_final: 0.8457 (mtt90) REVERT: C 17 GLN cc_start: 0.7265 (tm-30) cc_final: 0.7045 (tp40) REVERT: D 21 MET cc_start: 0.7201 (ptt) cc_final: 0.6988 (ptm) REVERT: D 42 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8481 (tm-30) REVERT: E 189 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8613 (mt) outliers start: 32 outliers final: 28 residues processed: 182 average time/residue: 0.1140 time to fit residues: 27.3729 Evaluate side-chains 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.1980 chunk 33 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115377 restraints weight = 12307.798| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.83 r_work: 0.3437 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8941 Z= 0.105 Angle : 0.533 7.568 12140 Z= 0.280 Chirality : 0.041 0.176 1385 Planarity : 0.003 0.043 1524 Dihedral : 4.706 28.763 1282 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.74 % Allowed : 17.20 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.16 (0.26), residues: 1103 helix: 1.09 (0.29), residues: 364 sheet: 0.07 (0.31), residues: 299 loop : -1.22 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.017 0.001 TYR B 302 PHE 0.010 0.001 PHE A 105 TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8938) covalent geometry : angle 0.53317 (12134) SS BOND : bond 0.00674 ( 3) SS BOND : angle 0.97172 ( 6) hydrogen bonds : bond 0.02995 ( 401) hydrogen bonds : angle 4.25300 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.327 Fit side-chains REVERT: A 36 PHE cc_start: 0.7931 (t80) cc_final: 0.6603 (m-10) REVERT: A 101 GLN cc_start: 0.6191 (mm-40) cc_final: 0.5789 (mm-40) REVERT: A 117 ASN cc_start: 0.8824 (m110) cc_final: 0.8472 (m-40) REVERT: A 134 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7954 (mtpt) REVERT: A 219 GLN cc_start: 0.7609 (tp40) cc_final: 0.7346 (tp40) REVERT: B 31 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8412 (mtt90) outliers start: 35 outliers final: 29 residues processed: 192 average time/residue: 0.1115 time to fit residues: 28.1416 Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109258 restraints weight = 11570.864| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.68 r_work: 0.3349 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8941 Z= 0.300 Angle : 0.700 9.660 12140 Z= 0.366 Chirality : 0.046 0.216 1385 Planarity : 0.004 0.042 1524 Dihedral : 5.322 28.446 1282 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.49 % Allowed : 17.52 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.53 (0.26), residues: 1103 helix: 0.76 (0.29), residues: 362 sheet: -0.12 (0.31), residues: 304 loop : -1.42 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 20 TYR 0.017 0.002 TYR B 302 PHE 0.019 0.002 PHE A 179 TRP 0.021 0.002 TRP E 47 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 8938) covalent geometry : angle 0.69940 (12134) SS BOND : bond 0.01351 ( 3) SS BOND : angle 1.30385 ( 6) hydrogen bonds : bond 0.04204 ( 401) hydrogen bonds : angle 4.79046 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.336 Fit side-chains REVERT: A 36 PHE cc_start: 0.7956 (t80) cc_final: 0.6624 (m-10) REVERT: A 101 GLN cc_start: 0.6269 (mm-40) cc_final: 0.5930 (mm-40) REVERT: A 117 ASN cc_start: 0.8865 (m110) cc_final: 0.8517 (m-40) REVERT: A 134 LYS cc_start: 0.8263 (mmtp) cc_final: 0.8033 (mtpt) REVERT: A 219 GLN cc_start: 0.7817 (tp40) cc_final: 0.7613 (tp40) REVERT: A 268 MET cc_start: 0.4239 (ttm) cc_final: 0.3088 (tpp) REVERT: A 281 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.4682 (t80) REVERT: B 31 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8488 (mtt90) REVERT: B 275 GLU cc_start: 0.5315 (mt-10) cc_final: 0.5109 (mt-10) REVERT: D 42 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8233 (mm-30) REVERT: E 189 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8696 (mt) outliers start: 42 outliers final: 31 residues processed: 182 average time/residue: 0.1041 time to fit residues: 25.1726 Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.130295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112024 restraints weight = 12136.263| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.78 r_work: 0.3389 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8941 Z= 0.149 Angle : 0.604 8.049 12140 Z= 0.317 Chirality : 0.042 0.184 1385 Planarity : 0.004 0.040 1524 Dihedral : 5.090 29.386 1282 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.31 % Allowed : 18.70 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1103 helix: 0.84 (0.29), residues: 362 sheet: -0.01 (0.31), residues: 291 loop : -1.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 20 TYR 0.016 0.001 TYR B 302 PHE 0.012 0.001 PHE A 179 TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8938) covalent geometry : angle 0.60370 (12134) SS BOND : bond 0.00915 ( 3) SS BOND : angle 1.09368 ( 6) hydrogen bonds : bond 0.03460 ( 401) hydrogen bonds : angle 4.53408 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.326 Fit side-chains REVERT: A 36 PHE cc_start: 0.7934 (t80) cc_final: 0.6625 (m-10) REVERT: A 101 GLN cc_start: 0.6203 (mm-40) cc_final: 0.5854 (mm-40) REVERT: A 117 ASN cc_start: 0.8841 (m110) cc_final: 0.8589 (m110) REVERT: A 134 LYS cc_start: 0.8260 (mmtp) cc_final: 0.8017 (mtpt) REVERT: A 268 MET cc_start: 0.4030 (ttm) cc_final: 0.2930 (tpp) REVERT: A 281 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.4684 (t80) REVERT: B 31 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8454 (mtt90) REVERT: C 17 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6972 (tp40) REVERT: D 42 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8261 (mm-30) REVERT: E 189 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8634 (mt) outliers start: 31 outliers final: 27 residues processed: 184 average time/residue: 0.1178 time to fit residues: 28.4591 Evaluate side-chains 193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112579 restraints weight = 12012.278| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.75 r_work: 0.3397 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8941 Z= 0.146 Angle : 0.596 7.983 12140 Z= 0.313 Chirality : 0.042 0.181 1385 Planarity : 0.004 0.040 1524 Dihedral : 4.988 28.866 1282 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.74 % Allowed : 18.48 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.39 (0.26), residues: 1103 helix: 0.90 (0.29), residues: 362 sheet: -0.01 (0.31), residues: 291 loop : -1.35 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 20 TYR 0.016 0.001 TYR B 302 PHE 0.011 0.001 PHE A 179 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8938) covalent geometry : angle 0.59534 (12134) SS BOND : bond 0.00881 ( 3) SS BOND : angle 1.06948 ( 6) hydrogen bonds : bond 0.03376 ( 401) hydrogen bonds : angle 4.47951 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.33 seconds wall clock time: 46 minutes 21.08 seconds (2781.08 seconds total)