Starting phenix.real_space_refine on Sat Aug 23 02:53:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhy_36300/08_2025/8jhy_36300.map" } resolution = 2.87 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= 0.024 sd= 0.106 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 69 5.16 5 C 5800 2.51 5 N 1542 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9073 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'IX8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9073 At special positions: 0 Unit cell: (91.8, 122.4, 133.45, 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 69 16.00 O 1662 8.00 N 1542 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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: 0.72 Conformation dependent library (CDL) restraints added in 216.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 33.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.609A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.545A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.998A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 4.016A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 3.643A pdb=" N ALA D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.738A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.604A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 260 removed outlier: 3.880A pdb=" N THR D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.536A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 329 through 351 removed outlier: 3.774A pdb=" N CYS D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.517A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.896A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 Proline residue: A 31 - end of helix removed outlier: 3.706A pdb=" N PHE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.704A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.876A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.082A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.429A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 4.318A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.006A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.754A pdb=" N ASN A 137 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 removed outlier: 4.106A pdb=" N ILE A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 188 through 215 removed outlier: 4.261A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.113A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.562A pdb=" N MET A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 261 removed outlier: 3.638A pdb=" N VAL A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.581A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.507A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 285 through 294 Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.758A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.649A 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: 6.956A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.996A 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 151 removed outlier: 6.622A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.275A 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: 4.255A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.669A 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: 6.551A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.504A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.600A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.501A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.457A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.971A pdb=" N ILE A 182 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 345 hydrogen bonds defined for protein. 951 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: 1.30 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1446 1.25 - 1.39: 2357 1.39 - 1.54: 5291 1.54 - 1.68: 80 1.68 - 1.83: 100 Bond restraints: 9274 Sorted by residual: bond pdb=" C9 IX8 A 401 " pdb=" N10 IX8 A 401 " ideal model delta sigma weight residual 1.386 1.265 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C27 IX8 A 401 " pdb=" C32 IX8 A 401 " ideal model delta sigma weight residual 1.396 1.277 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C4 IX8 A 401 " pdb=" O5 IX8 A 401 " ideal model delta sigma weight residual 1.221 1.105 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" CA TYR A 87 " pdb=" C TYR A 87 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.40e-02 5.10e+03 3.00e+01 bond pdb=" C GLU A 190 " pdb=" N ALA A 191 " ideal model delta sigma weight residual 1.335 1.270 0.065 1.30e-02 5.92e+03 2.48e+01 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 12420 3.48 - 6.95: 116 6.95 - 10.43: 11 10.43 - 13.91: 4 13.91 - 17.39: 2 Bond angle restraints: 12553 Sorted by residual: angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 112.96 106.51 6.45 1.00e+00 1.00e+00 4.17e+01 angle pdb=" C6 IX8 A 401 " pdb=" C4 IX8 A 401 " pdb=" N3 IX8 A 401 " ideal model delta sigma weight residual 114.73 132.12 -17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA HIS A 189 " pdb=" C HIS A 189 " pdb=" N GLU A 190 " ideal model delta sigma weight residual 117.82 110.18 7.64 1.42e+00 4.96e-01 2.89e+01 angle pdb=" C23 IX8 A 401 " pdb=" C22 IX8 A 401 " pdb=" C24 IX8 A 401 " ideal model delta sigma weight residual 110.88 95.45 15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" O HIS A 189 " pdb=" C HIS A 189 " pdb=" N GLU A 190 " ideal model delta sigma weight residual 122.33 129.19 -6.86 1.34e+00 5.57e-01 2.62e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 4918 15.89 - 31.77: 477 31.77 - 47.66: 118 47.66 - 63.55: 22 63.55 - 79.43: 11 Dihedral angle restraints: 5546 sinusoidal: 2234 harmonic: 3312 Sorted by residual: dihedral pdb=" CA SER A 62 " pdb=" C SER A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG S 38 " pdb=" C ARG S 38 " pdb=" N GLN S 39 " pdb=" CA GLN S 39 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1195 0.071 - 0.142: 202 0.142 - 0.213: 7 0.213 - 0.284: 2 0.284 - 0.355: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C13 CLR A 402 " pdb=" C12 CLR A 402 " pdb=" C14 CLR A 402 " pdb=" C17 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C10 CLR A 402 " pdb=" C1 CLR A 402 " pdb=" C5 CLR A 402 " pdb=" C9 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.59 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1405 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 IX8 A 401 " -0.015 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" C4 IX8 A 401 " 0.060 2.00e-02 2.50e+03 pdb=" C6 IX8 A 401 " -0.030 2.00e-02 2.50e+03 pdb=" N3 IX8 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" O5 IX8 A 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " 0.014 2.00e-02 2.50e+03 2.67e-02 7.14e+00 pdb=" C ASN A 86 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 86 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 87 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO S 75 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.034 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 116 2.64 - 3.21: 7970 3.21 - 3.77: 12747 3.77 - 4.34: 18608 4.34 - 4.90: 31442 Nonbonded interactions: 70883 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.078 3.040 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.140 3.120 nonbonded pdb=" O ALA C 56 " pdb=" NH1 ARG C 62 " model vdw 2.172 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.203 3.040 nonbonded pdb=" OG SER S 30 " pdb=" OD1 ASP S 74 " model vdw 2.214 3.040 ... (remaining 70878 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.007 0.121 9278 Z= 0.354 Angle : 0.965 17.386 12561 Z= 0.525 Chirality : 0.052 0.355 1408 Planarity : 0.005 0.061 1579 Dihedral : 13.896 79.432 3394 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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 aren not related in a simple way. whole: -2.25 (0.23), residues: 1130 helix: -1.74 (0.26), residues: 355 sheet: 0.08 (0.29), residues: 296 loop : -2.27 (0.23), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 90 TYR 0.021 0.003 TYR B 105 PHE 0.030 0.002 PHE B 234 TRP 0.020 0.003 TRP B 82 HIS 0.015 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00724 ( 9274) covalent geometry : angle 0.96448 (12553) SS BOND : bond 0.00631 ( 4) SS BOND : angle 1.43610 ( 8) hydrogen bonds : bond 0.17779 ( 345) hydrogen bonds : angle 6.70411 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.434 Fit side-chains REVERT: D 310 LEU cc_start: 0.8185 (mm) cc_final: 0.7896 (mt) REVERT: A 220 MET cc_start: 0.7790 (mtt) cc_final: 0.7392 (mtt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.5905 time to fit residues: 96.6022 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN D 255 ASN S 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112499 restraints weight = 14831.446| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.79 r_work: 0.3465 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9278 Z= 0.160 Angle : 0.690 10.596 12561 Z= 0.360 Chirality : 0.046 0.202 1408 Planarity : 0.005 0.051 1579 Dihedral : 6.879 64.445 1320 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.12 % Allowed : 11.26 % Favored : 87.63 % 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 aren not related in a simple way. whole: -1.60 (0.24), residues: 1130 helix: -1.03 (0.28), residues: 355 sheet: 0.32 (0.30), residues: 295 loop : -1.94 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 32 TYR 0.017 0.002 TYR B 105 PHE 0.018 0.002 PHE B 234 TRP 0.018 0.002 TRP B 82 HIS 0.009 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9274) covalent geometry : angle 0.68886 (12553) SS BOND : bond 0.00645 ( 4) SS BOND : angle 1.44847 ( 8) hydrogen bonds : bond 0.04791 ( 345) hydrogen bonds : angle 5.13796 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.221 Fit side-chains REVERT: D 310 LEU cc_start: 0.8164 (mm) cc_final: 0.7848 (mt) REVERT: S 118 THR cc_start: 0.7830 (t) cc_final: 0.7625 (p) REVERT: A 219 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7867 (mp10) outliers start: 11 outliers final: 2 residues processed: 146 average time/residue: 0.5508 time to fit residues: 85.4000 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 235 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.113349 restraints weight = 14706.588| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.78 r_work: 0.3471 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9278 Z= 0.137 Angle : 0.631 10.307 12561 Z= 0.330 Chirality : 0.044 0.221 1408 Planarity : 0.004 0.048 1579 Dihedral : 6.565 64.905 1320 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.42 % Allowed : 14.00 % Favored : 84.58 % 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 aren not related in a simple way. whole: -1.18 (0.25), residues: 1130 helix: -0.63 (0.29), residues: 358 sheet: 0.43 (0.30), residues: 291 loop : -1.63 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 32 TYR 0.015 0.002 TYR B 105 PHE 0.014 0.001 PHE B 234 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9274) covalent geometry : angle 0.63032 (12553) SS BOND : bond 0.00549 ( 4) SS BOND : angle 1.33081 ( 8) hydrogen bonds : bond 0.04191 ( 345) hydrogen bonds : angle 4.81969 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.357 Fit side-chains REVERT: C 29 LYS cc_start: 0.8255 (mmtp) cc_final: 0.8028 (mmtp) REVERT: D 243 MET cc_start: 0.8067 (ttp) cc_final: 0.7805 (ttm) REVERT: D 276 GLU cc_start: 0.6991 (mp0) cc_final: 0.6769 (mp0) REVERT: D 310 LEU cc_start: 0.8161 (mm) cc_final: 0.7812 (mt) REVERT: S 93 MET cc_start: 0.7068 (ptt) cc_final: 0.6851 (ttt) REVERT: A 40 PHE cc_start: 0.8007 (m-80) cc_final: 0.7674 (m-80) outliers start: 14 outliers final: 4 residues processed: 149 average time/residue: 0.5490 time to fit residues: 87.2734 Evaluate side-chains 138 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 91 optimal weight: 0.0470 chunk 31 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 188 HIS D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112187 restraints weight = 14907.592| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.80 r_work: 0.3457 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9278 Z= 0.154 Angle : 0.643 10.310 12561 Z= 0.334 Chirality : 0.045 0.233 1408 Planarity : 0.004 0.047 1579 Dihedral : 6.453 63.123 1320 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.23 % Allowed : 16.13 % Favored : 81.64 % 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 aren not related in a simple way. whole: -1.06 (0.25), residues: 1130 helix: -0.43 (0.29), residues: 352 sheet: 0.45 (0.31), residues: 285 loop : -1.57 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 180 TYR 0.016 0.002 TYR B 105 PHE 0.019 0.002 PHE D 354 TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9274) covalent geometry : angle 0.64268 (12553) SS BOND : bond 0.00571 ( 4) SS BOND : angle 1.35129 ( 8) hydrogen bonds : bond 0.04258 ( 345) hydrogen bonds : angle 4.78247 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.262 Fit side-chains REVERT: D 243 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7757 (ttm) REVERT: D 276 GLU cc_start: 0.7067 (mp0) cc_final: 0.6833 (mp0) REVERT: D 310 LEU cc_start: 0.8148 (mm) cc_final: 0.7805 (mt) outliers start: 22 outliers final: 10 residues processed: 144 average time/residue: 0.5377 time to fit residues: 82.6399 Evaluate side-chains 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114459 restraints weight = 14866.175| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.72 r_work: 0.3486 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9278 Z= 0.115 Angle : 0.592 9.639 12561 Z= 0.307 Chirality : 0.043 0.227 1408 Planarity : 0.004 0.046 1579 Dihedral : 5.984 60.723 1320 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.03 % Allowed : 17.44 % Favored : 80.53 % 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 aren not related in a simple way. whole: -0.82 (0.25), residues: 1130 helix: -0.18 (0.29), residues: 354 sheet: 0.61 (0.31), residues: 280 loop : -1.48 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 180 TYR 0.013 0.001 TYR S 190 PHE 0.018 0.001 PHE D 354 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9274) covalent geometry : angle 0.59089 (12553) SS BOND : bond 0.00482 ( 4) SS BOND : angle 1.25301 ( 8) hydrogen bonds : bond 0.03615 ( 345) hydrogen bonds : angle 4.57822 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.407 Fit side-chains REVERT: B 217 MET cc_start: 0.7601 (tpt) cc_final: 0.7399 (tpt) REVERT: D 243 MET cc_start: 0.8058 (ttp) cc_final: 0.7768 (ttm) REVERT: D 310 LEU cc_start: 0.8145 (mm) cc_final: 0.7796 (mt) REVERT: A 40 PHE cc_start: 0.8006 (m-80) cc_final: 0.7643 (m-80) REVERT: A 219 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7807 (mp10) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 0.5375 time to fit residues: 80.7745 Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 259 GLN B 340 ASN A 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115208 restraints weight = 14833.260| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.72 r_work: 0.3498 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9278 Z= 0.109 Angle : 0.579 9.892 12561 Z= 0.299 Chirality : 0.043 0.222 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.771 61.297 1320 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.03 % Allowed : 18.15 % Favored : 79.82 % 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 aren not related in a simple way. whole: -0.71 (0.25), residues: 1130 helix: 0.00 (0.30), residues: 355 sheet: 0.63 (0.31), residues: 281 loop : -1.46 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 32 TYR 0.012 0.001 TYR S 95 PHE 0.018 0.001 PHE D 354 TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9274) covalent geometry : angle 0.57827 (12553) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.18195 ( 8) hydrogen bonds : bond 0.03414 ( 345) hydrogen bonds : angle 4.48799 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.371 Fit side-chains REVERT: B 102 THR cc_start: 0.8653 (p) cc_final: 0.8336 (t) REVERT: B 259 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5830 (mp10) REVERT: D 243 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7772 (ttm) REVERT: D 310 LEU cc_start: 0.8126 (mm) cc_final: 0.7774 (mt) REVERT: S 67 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7189 (ttp-110) REVERT: A 40 PHE cc_start: 0.7996 (m-80) cc_final: 0.7677 (m-80) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.5510 time to fit residues: 79.4893 Evaluate side-chains 127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN A 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116188 restraints weight = 14878.152| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.72 r_work: 0.3515 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9278 Z= 0.099 Angle : 0.557 9.741 12561 Z= 0.288 Chirality : 0.042 0.219 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.656 61.199 1320 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.23 % Allowed : 18.46 % Favored : 79.31 % 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 aren not related in a simple way. whole: -0.57 (0.25), residues: 1130 helix: 0.16 (0.30), residues: 355 sheet: 0.67 (0.31), residues: 283 loop : -1.38 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 32 TYR 0.012 0.001 TYR S 190 PHE 0.016 0.001 PHE D 354 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9274) covalent geometry : angle 0.55686 (12553) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.15603 ( 8) hydrogen bonds : bond 0.03158 ( 345) hydrogen bonds : angle 4.37897 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.307 Fit side-chains REVERT: B 102 THR cc_start: 0.8629 (p) cc_final: 0.8336 (t) REVERT: B 259 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5943 (mp10) REVERT: C 29 LYS cc_start: 0.8272 (mmtp) cc_final: 0.8020 (mmtp) REVERT: D 310 LEU cc_start: 0.8103 (mm) cc_final: 0.7744 (mt) REVERT: A 40 PHE cc_start: 0.7976 (m-80) cc_final: 0.7615 (m-80) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.5138 time to fit residues: 76.2247 Evaluate side-chains 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.0050 chunk 23 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN B 340 ASN A 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.137770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114755 restraints weight = 14839.186| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.71 r_work: 0.3490 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9278 Z= 0.121 Angle : 0.602 10.200 12561 Z= 0.307 Chirality : 0.044 0.256 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.608 57.605 1320 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.43 % Allowed : 19.17 % Favored : 78.40 % 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 aren not related in a simple way. whole: -0.54 (0.25), residues: 1130 helix: 0.18 (0.30), residues: 355 sheet: 0.65 (0.31), residues: 282 loop : -1.34 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 32 TYR 0.011 0.001 TYR S 95 PHE 0.016 0.001 PHE D 354 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9274) covalent geometry : angle 0.60173 (12553) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.14301 ( 8) hydrogen bonds : bond 0.03564 ( 345) hydrogen bonds : angle 4.43091 ( 951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.346 Fit side-chains REVERT: B 102 THR cc_start: 0.8706 (p) cc_final: 0.8389 (t) REVERT: C 29 LYS cc_start: 0.8267 (mmtp) cc_final: 0.8020 (mmtp) REVERT: D 310 LEU cc_start: 0.8105 (mm) cc_final: 0.7736 (mt) REVERT: S 67 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7363 (mtp-110) REVERT: A 40 PHE cc_start: 0.7968 (m-80) cc_final: 0.7653 (m-80) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.5332 time to fit residues: 78.8778 Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN A 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115153 restraints weight = 14798.222| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.77 r_work: 0.3501 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9278 Z= 0.111 Angle : 0.580 9.909 12561 Z= 0.299 Chirality : 0.043 0.292 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.509 58.194 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 19.57 % Favored : 78.09 % 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 aren not related in a simple way. whole: -0.40 (0.25), residues: 1130 helix: 0.38 (0.30), residues: 350 sheet: 0.65 (0.31), residues: 284 loop : -1.28 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 32 TYR 0.010 0.001 TYR S 190 PHE 0.022 0.001 PHE S 32 TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9274) covalent geometry : angle 0.57997 (12553) SS BOND : bond 0.00466 ( 4) SS BOND : angle 1.09039 ( 8) hydrogen bonds : bond 0.03336 ( 345) hydrogen bonds : angle 4.37530 ( 951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.289 Fit side-chains REVERT: B 102 THR cc_start: 0.8669 (p) cc_final: 0.8361 (t) REVERT: C 29 LYS cc_start: 0.8253 (mmtp) cc_final: 0.8000 (mmtp) REVERT: D 310 LEU cc_start: 0.8091 (mm) cc_final: 0.7718 (mt) REVERT: S 67 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7373 (mtp-110) REVERT: A 11 LEU cc_start: 0.8113 (tt) cc_final: 0.7909 (tm) REVERT: A 40 PHE cc_start: 0.7935 (m-80) cc_final: 0.7586 (m-80) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.5235 time to fit residues: 78.2064 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115735 restraints weight = 14935.342| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.77 r_work: 0.3498 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9278 Z= 0.117 Angle : 0.600 11.570 12561 Z= 0.307 Chirality : 0.044 0.331 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.463 57.415 1320 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 19.98 % Favored : 77.89 % 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 aren not related in a simple way. whole: -0.34 (0.25), residues: 1130 helix: 0.49 (0.30), residues: 346 sheet: 0.66 (0.31), residues: 282 loop : -1.26 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 32 TYR 0.011 0.001 TYR S 95 PHE 0.026 0.001 PHE S 32 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9274) covalent geometry : angle 0.59991 (12553) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.10592 ( 8) hydrogen bonds : bond 0.03408 ( 345) hydrogen bonds : angle 4.38806 ( 951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.357 Fit side-chains REVERT: B 102 THR cc_start: 0.8686 (p) cc_final: 0.8382 (t) REVERT: C 29 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7990 (mmtp) REVERT: D 310 LEU cc_start: 0.8079 (mm) cc_final: 0.7726 (mt) REVERT: S 67 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7373 (mtp-110) REVERT: S 166 LEU cc_start: 0.7730 (tt) cc_final: 0.7524 (tp) REVERT: A 11 LEU cc_start: 0.8141 (tt) cc_final: 0.7919 (tm) REVERT: A 40 PHE cc_start: 0.7934 (m-80) cc_final: 0.7581 (m-80) outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 0.5117 time to fit residues: 73.9956 Evaluate side-chains 137 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN B 340 ASN A 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.115959 restraints weight = 14661.188| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.77 r_work: 0.3513 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9278 Z= 0.107 Angle : 0.587 12.326 12561 Z= 0.300 Chirality : 0.043 0.294 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.372 57.556 1320 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.03 % Allowed : 20.28 % Favored : 77.69 % 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 aren not related in a simple way. whole: -0.38 (0.26), residues: 1130 helix: 0.41 (0.30), residues: 354 sheet: 0.56 (0.31), residues: 294 loop : -1.24 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 32 TYR 0.010 0.001 TYR S 190 PHE 0.023 0.001 PHE S 32 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9274) covalent geometry : angle 0.58706 (12553) SS BOND : bond 0.00461 ( 4) SS BOND : angle 1.04074 ( 8) hydrogen bonds : bond 0.03188 ( 345) hydrogen bonds : angle 4.33075 ( 951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.67 seconds wall clock time: 59 minutes 53.15 seconds (3593.15 seconds total)