Starting phenix.real_space_refine on Wed Feb 4 03:00:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.map" model { file = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2026/7xwo_33497.cif" } resolution = 2.7 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= 0.024 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 60 5.16 5 C 5553 2.51 5 N 1499 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2041 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TRP:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2568 Classifications: {'peptide': 336} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1760 Classifications: {'peptide': 230} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 79 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 8725 At special positions: 0 Unit cell: (119.48, 118.656, 108.768, 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 60 16.00 O 1613 8.00 N 1499 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 199.4 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 32.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.744A pdb=" N ALA B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 35 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 4.050A pdb=" N ILE B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 86 removed outlier: 3.524A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.745A pdb=" N VAL B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.506A pdb=" N ILE B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.686A pdb=" N VAL B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.608A pdb=" N CYS B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.597A pdb=" N ILE B 202 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 226 removed outlier: 3.549A pdb=" N VAL B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 261 removed outlier: 3.578A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.648A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.832A pdb=" N ASN B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Proline residue: B 304 - end of helix removed outlier: 3.610A pdb=" N TYR B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 29 removed outlier: 3.589A pdb=" N GLU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.563A pdb=" N SER E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 25 removed outlier: 3.566A pdb=" N ARG F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 22 " --> pdb=" O MET F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 45 through 52 removed outlier: 3.519A pdb=" N ILE F 49 " --> pdb=" O GLY F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 260 through 270 removed outlier: 4.089A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 298 through 319 removed outlier: 3.913A pdb=" N PHE F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 358 removed outlier: 3.574A pdb=" N ASP F 348 " --> pdb=" O ASN F 344 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG F 356 " --> pdb=" O GLN F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 21 removed outlier: 3.942A pdb=" N LEU G 14 " --> pdb=" O GLN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.624A pdb=" N ASP G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 56 removed outlier: 6.587A pdb=" N ILE C 343 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR C 55 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 341 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 68 removed outlier: 3.934A pdb=" N ALA C 65 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 110 removed outlier: 5.935A pdb=" N CYS C 126 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU C 143 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 128 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 139 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.095A pdb=" N PHE C 156 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 183 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP C 175 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN C 181 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 192 through 197 removed outlier: 3.881A pdb=" N GLN C 225 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP C 217 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS C 223 " --> pdb=" O ASP C 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.528A pdb=" N MET C 267 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP C 259 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU C 265 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 278 through 283 removed outlier: 6.708A pdb=" N CYS C 299 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C 312 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 301 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 308 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.594A pdb=" N SER E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.581A pdb=" N THR E 114 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.681A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 184 through 190 removed outlier: 6.483A pdb=" N LEU F 34 " --> pdb=" O HIS F 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE F 199 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 222 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 39 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 190 removed outlier: 6.483A pdb=" N LEU F 34 " --> pdb=" O HIS F 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE F 199 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 222 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 39 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE F 257 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 223 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN F 259 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 225 " --> pdb=" O ASN F 259 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 942 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: 0.95 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2815 1.34 - 1.46: 2183 1.46 - 1.58: 3825 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8912 Sorted by residual: bond pdb=" C SER B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" CG LEU E 174 " pdb=" CD1 LEU E 174 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" N ARG C 155 " pdb=" CA ARG C 155 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.06e-02 8.90e+03 3.97e+00 bond pdb=" CA ARG C 155 " pdb=" C ARG C 155 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.24e-02 6.50e+03 3.76e+00 bond pdb=" CB VAL C 192 " pdb=" CG1 VAL C 192 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.29e+00 ... (remaining 8907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 11771 2.26 - 4.52: 279 4.52 - 6.78: 34 6.78 - 9.04: 9 9.04 - 11.30: 2 Bond angle restraints: 12095 Sorted by residual: angle pdb=" C VAL E 149 " pdb=" N THR E 150 " pdb=" CA THR E 150 " ideal model delta sigma weight residual 120.68 126.72 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " pdb=" CG TYR E 235 " ideal model delta sigma weight residual 113.90 106.81 7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 117.81 -8.00 2.21e+00 2.05e-01 1.31e+01 angle pdb=" C PRO E 40 " pdb=" N GLU E 41 " pdb=" CA GLU E 41 " ideal model delta sigma weight residual 122.46 127.51 -5.05 1.41e+00 5.03e-01 1.28e+01 ... (remaining 12090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4757 17.51 - 35.02: 412 35.02 - 52.54: 78 52.54 - 70.05: 7 70.05 - 87.56: 8 Dihedral angle restraints: 5262 sinusoidal: 1979 harmonic: 3283 Sorted by residual: dihedral pdb=" CA SER C 165 " pdb=" C SER C 165 " pdb=" N SER C 166 " pdb=" CA SER C 166 " ideal model delta harmonic sigma weight residual 180.00 133.36 46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA GLY C 315 " pdb=" C GLY C 315 " pdb=" N HIS C 316 " pdb=" CA HIS C 316 " ideal model delta harmonic sigma weight residual 180.00 146.42 33.58 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA LEU C 122 " pdb=" C LEU C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 934 0.052 - 0.104: 349 0.104 - 0.156: 73 0.156 - 0.208: 13 0.208 - 0.260: 4 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL B 183 " pdb=" CA VAL B 183 " pdb=" CG1 VAL B 183 " pdb=" CG2 VAL B 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR E 90 " pdb=" CA THR E 90 " pdb=" OG1 THR E 90 " pdb=" CG2 THR E 90 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1370 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 240 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO C 241 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 303 " 0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO B 304 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 145 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO B 146 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.040 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2376 2.80 - 3.32: 7105 3.32 - 3.85: 14535 3.85 - 4.37: 16936 4.37 - 4.90: 29372 Nonbonded interactions: 70324 Sorted by model distance: nonbonded pdb=" OH TYR B 206 " pdb=" O ALA B 260 " model vdw 2.275 3.040 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.288 3.040 nonbonded pdb=" OG SER C 286 " pdb=" OD2 ASP G 47 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU F 297 " pdb=" OG1 THR F 302 " model vdw 2.314 3.040 nonbonded pdb=" OG SER C 79 " pdb=" OD1 ASP C 81 " model vdw 2.320 3.040 ... (remaining 70319 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.090 Find NCS groups from input model: 0.020 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 0.067 8914 Z= 0.307 Angle : 0.868 11.295 12099 Z= 0.483 Chirality : 0.056 0.260 1373 Planarity : 0.008 0.075 1537 Dihedral : 13.885 87.562 3138 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.22 % Allowed : 6.09 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.88 (0.19), residues: 1108 helix: -4.90 (0.09), residues: 351 sheet: -1.51 (0.30), residues: 282 loop : -2.84 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 26 TYR 0.042 0.003 TYR B 93 PHE 0.029 0.003 PHE B 284 TRP 0.019 0.003 TRP B 156 HIS 0.008 0.002 HIS F 324 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 8912) covalent geometry : angle 0.86758 (12095) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.10804 ( 4) hydrogen bonds : bond 0.26911 ( 324) hydrogen bonds : angle 10.67589 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.337 Fit side-chains REVERT: B 28 MET cc_start: 0.4847 (mmm) cc_final: 0.4607 (mmm) REVERT: B 217 TYR cc_start: 0.7897 (m-80) cc_final: 0.7575 (m-80) REVERT: B 297 MET cc_start: 0.8391 (mmt) cc_final: 0.8062 (mmp) REVERT: C 75 LEU cc_start: 0.7854 (mt) cc_final: 0.7643 (mt) REVERT: C 160 ASN cc_start: 0.6271 (m-40) cc_final: 0.6065 (m-40) REVERT: C 308 ASP cc_start: 0.6858 (m-30) cc_final: 0.6654 (m-30) REVERT: E 85 LEU cc_start: 0.8692 (mm) cc_final: 0.8431 (mt) REVERT: F 239 ASP cc_start: 0.7125 (t0) cc_final: 0.6748 (t0) REVERT: F 247 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6328 (ttm110) REVERT: F 250 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.6552 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 215 average time/residue: 0.4354 time to fit residues: 100.6073 Evaluate side-chains 190 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 110 ASN B 140 GLN C 115 ASN C 345 ASN E 167 HIS ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN F 259 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.132381 restraints weight = 11612.465| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.79 r_work: 0.3692 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8914 Z= 0.198 Angle : 0.618 7.597 12099 Z= 0.331 Chirality : 0.045 0.254 1373 Planarity : 0.006 0.056 1537 Dihedral : 5.869 40.670 1224 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.81 % Allowed : 12.40 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.21), residues: 1108 helix: -3.17 (0.20), residues: 350 sheet: -0.89 (0.30), residues: 283 loop : -2.33 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 35 TYR 0.032 0.002 TYR E 235 PHE 0.042 0.002 PHE B 118 TRP 0.015 0.002 TRP B 156 HIS 0.010 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8912) covalent geometry : angle 0.61779 (12095) SS BOND : bond 0.00467 ( 2) SS BOND : angle 1.30173 ( 4) hydrogen bonds : bond 0.04752 ( 324) hydrogen bonds : angle 5.74507 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 28 MET cc_start: 0.5678 (mmm) cc_final: 0.5176 (mmm) REVERT: B 117 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7109 (ptm) REVERT: C 27 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7836 (mtt180) REVERT: C 160 ASN cc_start: 0.6362 (m-40) cc_final: 0.6138 (t0) REVERT: C 193 MET cc_start: 0.8188 (mmm) cc_final: 0.7853 (mmm) REVERT: C 224 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7635 (ptp90) REVERT: C 267 MET cc_start: 0.8191 (ttp) cc_final: 0.7978 (mtp) REVERT: C 308 ASP cc_start: 0.7371 (m-30) cc_final: 0.7144 (m-30) REVERT: E 85 LEU cc_start: 0.8738 (mm) cc_final: 0.8453 (mt) REVERT: F 262 ASP cc_start: 0.7883 (p0) cc_final: 0.7588 (p0) REVERT: F 276 GLU cc_start: 0.7070 (pm20) cc_final: 0.6621 (pm20) REVERT: F 337 GLU cc_start: 0.7311 (mp0) cc_final: 0.7094 (mp0) outliers start: 35 outliers final: 16 residues processed: 212 average time/residue: 0.5942 time to fit residues: 133.5557 Evaluate side-chains 205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 345 ASN F 204 GLN F 238 ASN F 246 ASN F 259 ASN F 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133450 restraints weight = 11467.367| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.77 r_work: 0.3712 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8914 Z= 0.158 Angle : 0.566 7.915 12099 Z= 0.301 Chirality : 0.044 0.230 1373 Planarity : 0.005 0.050 1537 Dihedral : 5.349 35.960 1224 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.81 % Allowed : 15.45 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.54 (0.23), residues: 1108 helix: -1.94 (0.25), residues: 350 sheet: -0.60 (0.30), residues: 276 loop : -2.04 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 47 TYR 0.029 0.002 TYR E 235 PHE 0.033 0.002 PHE B 118 TRP 0.011 0.002 TRP B 156 HIS 0.007 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8912) covalent geometry : angle 0.56624 (12095) SS BOND : bond 0.00368 ( 2) SS BOND : angle 1.00485 ( 4) hydrogen bonds : bond 0.03640 ( 324) hydrogen bonds : angle 5.01774 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.5623 (mmm) cc_final: 0.5232 (mmm) REVERT: B 117 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7073 (ptm) REVERT: B 136 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7760 (t) REVERT: B 270 PHE cc_start: 0.8675 (m-10) cc_final: 0.8274 (m-80) REVERT: C 27 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7847 (mtt180) REVERT: C 79 SER cc_start: 0.8047 (p) cc_final: 0.7836 (p) REVERT: C 186 THR cc_start: 0.8251 (p) cc_final: 0.8032 (m) REVERT: C 193 MET cc_start: 0.8158 (mmm) cc_final: 0.7855 (mmm) REVERT: C 267 MET cc_start: 0.8152 (ttp) cc_final: 0.7923 (ttm) REVERT: C 308 ASP cc_start: 0.7341 (m-30) cc_final: 0.7115 (m-30) REVERT: C 326 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7873 (p) REVERT: E 85 LEU cc_start: 0.8732 (mm) cc_final: 0.8415 (mt) REVERT: E 206 SER cc_start: 0.8303 (t) cc_final: 0.7985 (m) REVERT: F 239 ASP cc_start: 0.7782 (t0) cc_final: 0.7405 (t0) REVERT: F 281 GLU cc_start: 0.6329 (pm20) cc_final: 0.6014 (pm20) REVERT: F 284 ARG cc_start: 0.7529 (mpp80) cc_final: 0.7276 (mpp80) REVERT: F 337 GLU cc_start: 0.7260 (mp0) cc_final: 0.7014 (mp0) outliers start: 35 outliers final: 14 residues processed: 216 average time/residue: 0.5106 time to fit residues: 117.5148 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 311 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 115 ASN C 345 ASN F 259 ASN F 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135408 restraints weight = 11725.868| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.79 r_work: 0.3743 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8914 Z= 0.112 Angle : 0.526 6.836 12099 Z= 0.278 Chirality : 0.042 0.199 1373 Planarity : 0.004 0.046 1537 Dihedral : 4.900 30.039 1224 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.46 % Allowed : 16.21 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.24), residues: 1108 helix: -1.25 (0.27), residues: 351 sheet: -0.30 (0.31), residues: 269 loop : -1.82 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.026 0.001 TYR E 235 PHE 0.023 0.001 PHE B 118 TRP 0.009 0.001 TRP C 174 HIS 0.010 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8912) covalent geometry : angle 0.52594 (12095) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.80579 ( 4) hydrogen bonds : bond 0.03158 ( 324) hydrogen bonds : angle 4.71889 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 136 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7771 (t) REVERT: B 270 PHE cc_start: 0.8650 (m-10) cc_final: 0.8174 (m-80) REVERT: C 27 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7808 (mtt180) REVERT: C 139 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7429 (mtm180) REVERT: C 193 MET cc_start: 0.8145 (mmm) cc_final: 0.7862 (mmm) REVERT: C 224 ARG cc_start: 0.7749 (ptp-110) cc_final: 0.7465 (ptp90) REVERT: C 233 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: C 267 MET cc_start: 0.8181 (ttp) cc_final: 0.7943 (ttm) REVERT: C 308 ASP cc_start: 0.7358 (m-30) cc_final: 0.7128 (m-30) REVERT: C 326 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7855 (m) REVERT: C 332 VAL cc_start: 0.8120 (t) cc_final: 0.7909 (t) REVERT: E 206 SER cc_start: 0.8294 (t) cc_final: 0.7967 (m) REVERT: F 239 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7395 (t0) REVERT: F 250 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7400 (mtm-85) REVERT: F 281 GLU cc_start: 0.6351 (pm20) cc_final: 0.6043 (pm20) REVERT: F 284 ARG cc_start: 0.7602 (mpp80) cc_final: 0.7290 (mpp80) REVERT: F 337 GLU cc_start: 0.7285 (mp0) cc_final: 0.7023 (mp0) outliers start: 41 outliers final: 19 residues processed: 216 average time/residue: 0.5696 time to fit residues: 130.8420 Evaluate side-chains 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 311 GLU Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN C 345 ASN E 142 GLN F 352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.134578 restraints weight = 11661.838| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.79 r_work: 0.3725 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8914 Z= 0.151 Angle : 0.554 6.909 12099 Z= 0.290 Chirality : 0.044 0.218 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.918 32.875 1224 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.01 % Allowed : 17.08 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.24), residues: 1108 helix: -0.93 (0.28), residues: 350 sheet: -0.19 (0.30), residues: 267 loop : -1.67 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.029 0.002 TYR E 235 PHE 0.021 0.001 PHE B 284 TRP 0.010 0.002 TRP C 216 HIS 0.010 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8912) covalent geometry : angle 0.55430 (12095) SS BOND : bond 0.00397 ( 2) SS BOND : angle 0.94121 ( 4) hydrogen bonds : bond 0.03185 ( 324) hydrogen bonds : angle 4.64483 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6686 (tm) REVERT: B 117 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7081 (ptm) REVERT: B 136 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7749 (t) REVERT: B 270 PHE cc_start: 0.8618 (m-10) cc_final: 0.8302 (m-80) REVERT: C 27 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7793 (mtt180) REVERT: C 47 ARG cc_start: 0.7148 (tpt90) cc_final: 0.6857 (tpt90) REVERT: C 48 ILE cc_start: 0.8279 (mt) cc_final: 0.8017 (mt) REVERT: C 139 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7430 (mtm180) REVERT: C 224 ARG cc_start: 0.7838 (ptp-110) cc_final: 0.7524 (ptp90) REVERT: C 233 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: C 308 ASP cc_start: 0.7358 (m-30) cc_final: 0.7131 (m-30) REVERT: E 206 SER cc_start: 0.8305 (t) cc_final: 0.7978 (m) REVERT: F 239 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7435 (t0) REVERT: F 284 ARG cc_start: 0.7632 (mpp80) cc_final: 0.7277 (mpp80) REVERT: F 352 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7976 (mp10) outliers start: 46 outliers final: 24 residues processed: 217 average time/residue: 0.4790 time to fit residues: 110.5476 Evaluate side-chains 231 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 142 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131634 restraints weight = 11642.337| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.79 r_work: 0.3690 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8914 Z= 0.252 Angle : 0.623 8.079 12099 Z= 0.327 Chirality : 0.047 0.260 1373 Planarity : 0.005 0.046 1537 Dihedral : 5.364 37.343 1224 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.33 % Allowed : 17.74 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.24), residues: 1108 helix: -0.89 (0.28), residues: 352 sheet: -0.36 (0.30), residues: 286 loop : -1.58 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 300 TYR 0.032 0.002 TYR E 235 PHE 0.028 0.002 PHE B 118 TRP 0.013 0.002 TRP B 156 HIS 0.009 0.002 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 8912) covalent geometry : angle 0.62249 (12095) SS BOND : bond 0.00500 ( 2) SS BOND : angle 1.31622 ( 4) hydrogen bonds : bond 0.03601 ( 324) hydrogen bonds : angle 4.86536 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.273 Fit side-chains REVERT: B 33 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.6660 (tm) REVERT: B 136 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7829 (t) REVERT: C 27 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7782 (mtt180) REVERT: C 47 ARG cc_start: 0.7292 (tpt90) cc_final: 0.7069 (tpt90) REVERT: C 48 ILE cc_start: 0.8307 (mt) cc_final: 0.8081 (mm) REVERT: C 139 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7449 (mtm180) REVERT: C 147 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8092 (t70) REVERT: C 267 MET cc_start: 0.8134 (ttm) cc_final: 0.7883 (tpp) REVERT: C 308 ASP cc_start: 0.7356 (m-30) cc_final: 0.7106 (m-30) REVERT: E 37 ARG cc_start: 0.8405 (ptp-170) cc_final: 0.8156 (ptp-170) REVERT: E 180 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7716 (mtt-85) REVERT: E 206 SER cc_start: 0.8349 (t) cc_final: 0.8002 (m) REVERT: F 239 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7433 (t0) REVERT: F 250 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: F 284 ARG cc_start: 0.7704 (mpp80) cc_final: 0.7278 (mpp80) REVERT: F 341 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7941 (mpt-90) REVERT: F 352 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7986 (mp10) outliers start: 49 outliers final: 25 residues processed: 215 average time/residue: 0.4988 time to fit residues: 114.1352 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 282 HIS C 115 ASN C 345 ASN E 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133385 restraints weight = 11597.852| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.80 r_work: 0.3719 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8914 Z= 0.157 Angle : 0.568 8.089 12099 Z= 0.296 Chirality : 0.044 0.229 1373 Planarity : 0.004 0.044 1537 Dihedral : 5.063 33.302 1224 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.90 % Allowed : 18.82 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.25), residues: 1108 helix: -0.67 (0.28), residues: 352 sheet: -0.34 (0.30), residues: 275 loop : -1.44 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.029 0.001 TYR E 235 PHE 0.027 0.002 PHE B 284 TRP 0.010 0.002 TRP B 156 HIS 0.008 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8912) covalent geometry : angle 0.56814 (12095) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.01618 ( 4) hydrogen bonds : bond 0.03201 ( 324) hydrogen bonds : angle 4.72072 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.254 Fit side-chains REVERT: B 33 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6570 (tm) REVERT: B 57 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.6014 (tt) REVERT: B 117 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7064 (ptm) REVERT: B 136 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (t) REVERT: C 27 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7800 (mtt180) REVERT: C 47 ARG cc_start: 0.7224 (tpt90) cc_final: 0.7014 (tpt90) REVERT: C 48 ILE cc_start: 0.8303 (mt) cc_final: 0.8089 (mm) REVERT: C 139 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7428 (mtm180) REVERT: C 147 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.8111 (t70) REVERT: C 217 ASP cc_start: 0.8243 (t0) cc_final: 0.7785 (t0) REVERT: C 224 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7213 (ptp90) REVERT: C 233 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: C 267 MET cc_start: 0.8073 (ttm) cc_final: 0.7848 (tpp) REVERT: C 308 ASP cc_start: 0.7362 (m-30) cc_final: 0.7127 (m-30) REVERT: E 37 ARG cc_start: 0.8337 (ptp-170) cc_final: 0.8088 (ptp-170) REVERT: E 180 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7683 (mtt-85) REVERT: E 206 SER cc_start: 0.8327 (t) cc_final: 0.7992 (m) REVERT: F 230 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: F 239 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7423 (t0) REVERT: F 250 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7501 (mtm-85) REVERT: F 284 ARG cc_start: 0.7682 (mpp80) cc_final: 0.7320 (mpp80) REVERT: F 352 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7978 (mp10) outliers start: 45 outliers final: 23 residues processed: 222 average time/residue: 0.5812 time to fit residues: 136.5139 Evaluate side-chains 226 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.0570 chunk 40 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 115 ASN C 345 ASN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.149733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134655 restraints weight = 11595.591| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.79 r_work: 0.3735 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8914 Z= 0.123 Angle : 0.550 8.635 12099 Z= 0.285 Chirality : 0.043 0.202 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.790 29.577 1224 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.24 % Allowed : 20.57 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.25), residues: 1108 helix: -0.54 (0.29), residues: 351 sheet: -0.23 (0.30), residues: 272 loop : -1.32 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.027 0.001 TYR E 235 PHE 0.020 0.001 PHE B 118 TRP 0.009 0.001 TRP C 216 HIS 0.009 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8912) covalent geometry : angle 0.54987 (12095) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.77183 ( 4) hydrogen bonds : bond 0.02992 ( 324) hydrogen bonds : angle 4.62568 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.319 Fit side-chains REVERT: B 33 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6566 (tm) REVERT: B 136 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7797 (t) REVERT: B 205 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6853 (mt) REVERT: C 27 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7783 (mtt180) REVERT: C 139 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7418 (mtm180) REVERT: C 193 MET cc_start: 0.8087 (mmm) cc_final: 0.7830 (mmm) REVERT: C 217 ASP cc_start: 0.8240 (t0) cc_final: 0.7807 (t0) REVERT: C 224 ARG cc_start: 0.7737 (ptp90) cc_final: 0.7237 (ptp90) REVERT: C 233 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: C 267 MET cc_start: 0.8036 (ttm) cc_final: 0.7821 (tpp) REVERT: C 308 ASP cc_start: 0.7363 (m-30) cc_final: 0.7133 (m-30) REVERT: E 206 SER cc_start: 0.8369 (t) cc_final: 0.8037 (m) REVERT: F 230 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: F 239 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7411 (t0) REVERT: F 250 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: F 284 ARG cc_start: 0.7730 (mpp80) cc_final: 0.7365 (mpp80) REVERT: F 341 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7938 (mpt-90) REVERT: F 352 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7939 (mp10) outliers start: 39 outliers final: 21 residues processed: 196 average time/residue: 0.5298 time to fit residues: 110.6651 Evaluate side-chains 204 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 0.0470 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 115 ASN C 345 ASN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134487 restraints weight = 11569.139| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.78 r_work: 0.3728 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8914 Z= 0.139 Angle : 0.561 9.745 12099 Z= 0.289 Chirality : 0.044 0.209 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.811 30.165 1224 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.46 % Allowed : 20.13 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1108 helix: -0.40 (0.28), residues: 354 sheet: -0.28 (0.30), residues: 274 loop : -1.30 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.028 0.001 TYR E 235 PHE 0.022 0.001 PHE B 118 TRP 0.010 0.002 TRP F 211 HIS 0.007 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8912) covalent geometry : angle 0.56062 (12095) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.95230 ( 4) hydrogen bonds : bond 0.03037 ( 324) hydrogen bonds : angle 4.60216 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.321 Fit side-chains REVERT: B 33 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6546 (tm) REVERT: B 136 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 205 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.6919 (mt) REVERT: C 27 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7796 (mtt180) REVERT: C 139 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7398 (mtm180) REVERT: C 193 MET cc_start: 0.8095 (mmm) cc_final: 0.7831 (mmm) REVERT: C 224 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7265 (ptp90) REVERT: C 233 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: C 308 ASP cc_start: 0.7365 (m-30) cc_final: 0.7139 (m-30) REVERT: E 206 SER cc_start: 0.8371 (t) cc_final: 0.8060 (m) REVERT: F 230 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: F 239 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7416 (t0) REVERT: F 250 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7539 (mtm-85) REVERT: F 284 ARG cc_start: 0.7742 (mpp80) cc_final: 0.7402 (mpp80) REVERT: F 341 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7938 (mpt-90) REVERT: F 352 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7988 (mp10) outliers start: 41 outliers final: 25 residues processed: 196 average time/residue: 0.5319 time to fit residues: 111.0144 Evaluate side-chains 205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 110 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.0050 chunk 3 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 115 ASN C 345 ASN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.151627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136640 restraints weight = 11534.712| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.78 r_work: 0.3761 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8914 Z= 0.100 Angle : 0.533 9.758 12099 Z= 0.274 Chirality : 0.042 0.177 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.540 24.944 1224 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.70 % Allowed : 20.78 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.25), residues: 1108 helix: -0.13 (0.29), residues: 355 sheet: -0.21 (0.30), residues: 272 loop : -1.15 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.024 0.001 TYR E 235 PHE 0.019 0.001 PHE B 118 TRP 0.009 0.001 TRP C 68 HIS 0.006 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8912) covalent geometry : angle 0.53262 (12095) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.73691 ( 4) hydrogen bonds : bond 0.02843 ( 324) hydrogen bonds : angle 4.49031 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.339 Fit side-chains REVERT: B 33 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6528 (tm) REVERT: B 82 MET cc_start: 0.6679 (mtm) cc_final: 0.6285 (mtm) REVERT: B 136 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 205 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6689 (mt) REVERT: B 217 TYR cc_start: 0.7904 (m-80) cc_final: 0.7591 (m-80) REVERT: C 27 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7828 (mtt180) REVERT: C 139 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7397 (mtm180) REVERT: C 193 MET cc_start: 0.8052 (mmm) cc_final: 0.7805 (mmm) REVERT: C 308 ASP cc_start: 0.7338 (m-30) cc_final: 0.7114 (m-30) REVERT: E 206 SER cc_start: 0.8403 (t) cc_final: 0.8078 (m) REVERT: F 230 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: F 239 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7434 (t0) REVERT: F 250 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: F 284 ARG cc_start: 0.7729 (mpp80) cc_final: 0.7389 (mpp80) REVERT: F 341 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7909 (mpt-90) outliers start: 34 outliers final: 15 residues processed: 207 average time/residue: 0.5320 time to fit residues: 117.9298 Evaluate side-chains 201 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 109 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 115 ASN E 142 GLN E 194 ASN F 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135814 restraints weight = 11498.822| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.76 r_work: 0.3747 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8914 Z= 0.130 Angle : 0.554 10.076 12099 Z= 0.285 Chirality : 0.043 0.193 1373 Planarity : 0.004 0.048 1537 Dihedral : 4.660 27.111 1224 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.48 % Allowed : 21.98 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.25), residues: 1108 helix: -0.12 (0.29), residues: 355 sheet: -0.25 (0.30), residues: 272 loop : -1.16 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.027 0.001 TYR E 235 PHE 0.024 0.002 PHE F 240 TRP 0.009 0.001 TRP F 211 HIS 0.006 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8912) covalent geometry : angle 0.55387 (12095) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.85289 ( 4) hydrogen bonds : bond 0.02947 ( 324) hydrogen bonds : angle 4.49189 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.73 seconds wall clock time: 62 minutes 18.40 seconds (3738.40 seconds total)