Starting phenix.real_space_refine on Thu Feb 13 04:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xwo_33497/02_2025/7xwo_33497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xwo_33497/02_2025/7xwo_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_2025/7xwo_33497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2025/7xwo_33497.map" model { file = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2025/7xwo_33497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xwo_33497/02_2025/7xwo_33497.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 6} 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: 5.14, per 1000 atoms: 0.59 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: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.00 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: 2.46 Time building geometry restraints manager: 2.39 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: 1.390 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- 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 8912 Z= 0.456 Angle : 0.868 11.295 12095 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP B 156 HIS 0.008 0.002 HIS F 324 PHE 0.029 0.003 PHE B 284 TYR 0.042 0.003 TYR B 93 ARG 0.004 0.000 ARG G 26 *********************** 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 : 0.976 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: 0.8430 (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: 1.1178 time to fit residues: 257.9986 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 : 0.985 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.5980 chunk 84 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.3762 ------------------------------------------------------------------------------- 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 F 238 ASN F 259 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.149896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134919 restraints weight = 11499.579| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.78 r_work: 0.3737 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8912 Z= 0.173 Angle : 0.564 6.806 12095 Z= 0.302 Chirality : 0.042 0.214 1373 Planarity : 0.005 0.053 1537 Dihedral : 5.480 37.024 1224 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.94 % Allowed : 13.28 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.22), residues: 1108 helix: -3.07 (0.20), residues: 347 sheet: -0.79 (0.30), residues: 279 loop : -2.22 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 174 HIS 0.010 0.001 HIS E 167 PHE 0.039 0.001 PHE B 118 TYR 0.028 0.001 TYR E 235 ARG 0.004 0.000 ARG F 35 *********************** 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 224 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.5663 (mmm) cc_final: 0.5104 (mmm) REVERT: B 117 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7078 (ptm) REVERT: B 136 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7922 (t) REVERT: C 27 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7844 (mtt180) REVERT: C 193 MET cc_start: 0.8175 (mmm) cc_final: 0.7849 (mmm) REVERT: C 267 MET cc_start: 0.8108 (ttp) cc_final: 0.7903 (mtp) REVERT: C 308 ASP cc_start: 0.7367 (m-30) cc_final: 0.7126 (m-30) REVERT: F 262 ASP cc_start: 0.7863 (p0) cc_final: 0.7533 (p0) REVERT: F 276 GLU cc_start: 0.7012 (pm20) cc_final: 0.6638 (pm20) REVERT: F 337 GLU cc_start: 0.7273 (mp0) cc_final: 0.7067 (mp0) outliers start: 27 outliers final: 8 residues processed: 209 average time/residue: 1.2689 time to fit residues: 281.9350 Evaluate side-chains 199 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 42 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 193 SER 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 30 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 238 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 = 0.3996 r_free = 0.3996 target = 0.148873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133848 restraints weight = 11672.990| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.80 r_work: 0.3721 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8912 Z= 0.237 Angle : 0.562 7.136 12095 Z= 0.298 Chirality : 0.044 0.226 1373 Planarity : 0.005 0.050 1537 Dihedral : 5.259 37.160 1224 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.70 % Allowed : 15.89 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.23), residues: 1108 helix: -1.86 (0.25), residues: 352 sheet: -0.48 (0.30), residues: 269 loop : -2.02 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 174 HIS 0.007 0.001 HIS F 197 PHE 0.022 0.002 PHE B 118 TYR 0.029 0.002 TYR E 235 ARG 0.010 0.001 ARG C 47 *********************** 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 227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 28 MET cc_start: 0.5656 (mmm) cc_final: 0.5257 (mmm) REVERT: B 136 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7833 (t) REVERT: C 27 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7846 (mtt180) REVERT: C 79 SER cc_start: 0.8043 (p) cc_final: 0.7842 (p) REVERT: C 186 THR cc_start: 0.8257 (p) cc_final: 0.8050 (m) REVERT: C 193 MET cc_start: 0.8139 (mmm) cc_final: 0.7889 (mmm) REVERT: C 217 ASP cc_start: 0.8152 (t0) cc_final: 0.7913 (t0) REVERT: C 224 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7107 (ptp90) REVERT: C 267 MET cc_start: 0.8174 (ttp) cc_final: 0.7931 (ttm) REVERT: C 308 ASP cc_start: 0.7354 (m-30) cc_final: 0.7114 (m-30) REVERT: C 326 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7906 (p) REVERT: E 85 LEU cc_start: 0.8806 (mt) cc_final: 0.8582 (mm) REVERT: E 206 SER cc_start: 0.8335 (t) cc_final: 0.8001 (m) REVERT: F 239 ASP cc_start: 0.7786 (t0) cc_final: 0.7401 (t0) REVERT: F 329 HIS cc_start: 0.8401 (m-70) cc_final: 0.8183 (m-70) outliers start: 34 outliers final: 13 residues processed: 212 average time/residue: 1.2179 time to fit residues: 274.7590 Evaluate side-chains 205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 282 HIS 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 268 THR 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 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 345 ASN F 238 ASN F 259 ASN F 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.150248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135325 restraints weight = 11565.344| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.79 r_work: 0.3742 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8912 Z= 0.170 Angle : 0.532 7.580 12095 Z= 0.280 Chirality : 0.043 0.201 1373 Planarity : 0.004 0.046 1537 Dihedral : 4.852 32.078 1224 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.92 % Allowed : 17.30 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1108 helix: -1.13 (0.27), residues: 351 sheet: -0.29 (0.31), residues: 269 loop : -1.78 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.010 0.001 HIS F 197 PHE 0.026 0.001 PHE B 118 TYR 0.027 0.001 TYR E 235 ARG 0.005 0.000 ARG F 35 *********************** 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 229 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7059 (ptm) REVERT: B 136 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7886 (t) REVERT: B 217 TYR cc_start: 0.7944 (m-80) cc_final: 0.7627 (m-80) REVERT: C 27 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7813 (mtt180) REVERT: C 81 ASP cc_start: 0.7596 (p0) cc_final: 0.7353 (p0) REVERT: C 139 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7397 (mtm180) REVERT: C 193 MET cc_start: 0.8130 (mmm) cc_final: 0.7876 (mmm) REVERT: C 233 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: C 267 MET cc_start: 0.8194 (ttp) cc_final: 0.7952 (ttm) REVERT: C 308 ASP cc_start: 0.7386 (m-30) cc_final: 0.7151 (m-30) REVERT: E 85 LEU cc_start: 0.8757 (mt) cc_final: 0.8549 (mm) REVERT: E 206 SER cc_start: 0.8300 (t) cc_final: 0.7980 (m) REVERT: F 239 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7433 (t0) REVERT: F 329 HIS cc_start: 0.8298 (m-70) cc_final: 0.8090 (m-70) REVERT: F 352 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7948 (mp10) outliers start: 36 outliers final: 15 residues processed: 212 average time/residue: 1.2330 time to fit residues: 278.4150 Evaluate side-chains 205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 279 ILE 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 175 ASP 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 341 LEU 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 184 ILE Chi-restraints excluded: chain F residue 239 ASP 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 97 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134579 restraints weight = 11576.389| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.79 r_work: 0.3735 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8912 Z= 0.210 Angle : 0.551 7.546 12095 Z= 0.288 Chirality : 0.043 0.208 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.810 32.789 1224 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.03 % Allowed : 19.26 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1108 helix: -0.82 (0.28), residues: 351 sheet: -0.15 (0.31), residues: 267 loop : -1.63 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 216 HIS 0.009 0.001 HIS F 197 PHE 0.022 0.001 PHE B 118 TYR 0.028 0.001 TYR E 235 ARG 0.008 0.000 ARG F 35 *********************** 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 228 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.057 Fit side-chains REVERT: B 33 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.6799 (tm) REVERT: B 117 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6980 (ptm) REVERT: B 136 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7915 (t) REVERT: B 217 TYR cc_start: 0.8002 (m-80) cc_final: 0.7666 (m-80) REVERT: C 27 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7757 (mtt180) REVERT: C 122 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7688 (mt) REVERT: C 139 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7381 (mtm180) REVERT: C 193 MET cc_start: 0.8131 (mmm) cc_final: 0.7861 (mmm) REVERT: C 233 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: C 267 MET cc_start: 0.8217 (ttp) cc_final: 0.7998 (ttm) REVERT: C 308 ASP cc_start: 0.7383 (m-30) cc_final: 0.7143 (m-30) REVERT: E 85 LEU cc_start: 0.8752 (mt) cc_final: 0.8542 (mm) REVERT: E 206 SER cc_start: 0.8307 (t) cc_final: 0.7980 (m) REVERT: F 239 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7394 (t0) REVERT: F 250 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: F 284 ARG cc_start: 0.7883 (mpp80) cc_final: 0.7671 (mpp80) REVERT: F 329 HIS cc_start: 0.8317 (m-70) cc_final: 0.8091 (m-70) REVERT: F 352 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7955 (mp10) outliers start: 37 outliers final: 20 residues processed: 212 average time/residue: 1.2364 time to fit residues: 278.9704 Evaluate side-chains 222 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU 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 C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 122 LEU 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 C residue 345 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 26 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4019 r_free = 0.4019 target = 0.150298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135348 restraints weight = 11463.851| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.77 r_work: 0.3749 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8912 Z= 0.176 Angle : 0.540 9.449 12095 Z= 0.279 Chirality : 0.043 0.196 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.662 29.264 1224 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.79 % Allowed : 18.82 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1108 helix: -0.54 (0.28), residues: 351 sheet: -0.16 (0.30), residues: 272 loop : -1.46 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 68 HIS 0.007 0.001 HIS F 197 PHE 0.021 0.001 PHE B 118 TYR 0.026 0.001 TYR E 235 ARG 0.007 0.000 ARG F 35 *********************** 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: 44 poor density : 190 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6643 (tm) REVERT: B 40 TYR cc_start: 0.6825 (m-80) cc_final: 0.6508 (m-80) REVERT: B 117 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7028 (ptm) REVERT: B 217 TYR cc_start: 0.7940 (m-80) cc_final: 0.7633 (m-80) REVERT: B 261 ILE cc_start: 0.7797 (pt) cc_final: 0.7590 (mp) REVERT: C 27 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7778 (mtt180) REVERT: C 122 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 139 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7386 (mtm180) REVERT: C 193 MET cc_start: 0.8124 (mmm) cc_final: 0.7883 (mmm) REVERT: C 233 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: C 308 ASP cc_start: 0.7350 (m-30) cc_final: 0.7121 (m-30) REVERT: E 206 SER cc_start: 0.8320 (t) cc_final: 0.8010 (m) REVERT: F 239 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7396 (t0) REVERT: F 329 HIS cc_start: 0.8317 (m-70) cc_final: 0.8082 (m-70) REVERT: F 352 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7974 (mp10) outliers start: 44 outliers final: 21 residues processed: 216 average time/residue: 1.1500 time to fit residues: 266.2104 Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 125 THR 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 224 LEU Chi-restraints excluded: chain B residue 252 MET 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 122 LEU 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 268 THR Chi-restraints excluded: chain C residue 282 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 193 SER Chi-restraints excluded: chain E residue 215 THR 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 92 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134795 restraints weight = 11721.797| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.80 r_work: 0.3739 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8912 Z= 0.218 Angle : 0.565 9.502 12095 Z= 0.291 Chirality : 0.043 0.202 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.679 31.002 1223 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.46 % Allowed : 19.37 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1108 helix: -0.34 (0.29), residues: 350 sheet: -0.12 (0.30), residues: 272 loop : -1.43 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 174 HIS 0.007 0.001 HIS B 282 PHE 0.020 0.002 PHE F 240 TYR 0.027 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 *********************** 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 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.893 Fit side-chains REVERT: B 33 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6683 (tm) REVERT: B 245 MET cc_start: 0.6722 (ppp) cc_final: 0.6417 (tmt) REVERT: B 261 ILE cc_start: 0.7864 (pt) cc_final: 0.7651 (mp) REVERT: C 27 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7791 (mtt180) REVERT: C 122 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7913 (mt) REVERT: C 139 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7424 (mtm180) REVERT: C 222 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6918 (pmt) REVERT: C 308 ASP cc_start: 0.7368 (m-30) cc_final: 0.7140 (m-30) REVERT: E 206 SER cc_start: 0.8338 (t) cc_final: 0.8034 (m) REVERT: F 239 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7465 (t0) REVERT: F 250 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: F 281 GLU cc_start: 0.6273 (pm20) cc_final: 0.6023 (pm20) REVERT: F 300 ARG cc_start: 0.7249 (mtm180) cc_final: 0.6923 (mtm180) REVERT: F 329 HIS cc_start: 0.8297 (m-70) cc_final: 0.8019 (m-70) REVERT: F 352 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8008 (mp10) outliers start: 41 outliers final: 23 residues processed: 204 average time/residue: 1.1840 time to fit residues: 257.5782 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 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 122 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET 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 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 18 MET 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 38 optimal weight: 0.3980 chunk 56 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.149806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.134652 restraints weight = 11662.351| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.80 r_work: 0.3732 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8912 Z= 0.230 Angle : 0.574 9.742 12095 Z= 0.294 Chirality : 0.044 0.209 1373 Planarity : 0.004 0.041 1537 Dihedral : 4.732 31.706 1223 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.35 % Allowed : 19.59 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1108 helix: -0.24 (0.29), residues: 354 sheet: -0.15 (0.30), residues: 274 loop : -1.39 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 174 HIS 0.007 0.001 HIS F 197 PHE 0.020 0.002 PHE B 118 TYR 0.028 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 *********************** 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 228 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.892 Fit side-chains REVERT: B 33 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6646 (tm) REVERT: B 261 ILE cc_start: 0.7885 (pt) cc_final: 0.7658 (mp) REVERT: C 27 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7811 (mtt180) REVERT: C 122 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7928 (mt) REVERT: C 139 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7422 (mtm180) REVERT: C 222 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6788 (pmt) REVERT: C 233 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: C 308 ASP cc_start: 0.7430 (m-30) cc_final: 0.7203 (m-30) REVERT: E 206 SER cc_start: 0.8344 (t) cc_final: 0.8036 (m) REVERT: F 239 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7488 (t0) REVERT: F 250 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: F 329 HIS cc_start: 0.8311 (m-70) cc_final: 0.8078 (m-70) REVERT: F 352 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8040 (mp10) outliers start: 40 outliers final: 24 residues processed: 213 average time/residue: 1.2301 time to fit residues: 278.7745 Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 122 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 222 MET 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 192 MET Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135333 restraints weight = 11647.937| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.79 r_work: 0.3744 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8912 Z= 0.194 Angle : 0.553 8.695 12095 Z= 0.283 Chirality : 0.043 0.191 1373 Planarity : 0.004 0.041 1537 Dihedral : 4.606 29.800 1223 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.13 % Allowed : 20.13 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1108 helix: -0.07 (0.29), residues: 354 sheet: -0.03 (0.30), residues: 270 loop : -1.35 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.006 0.001 HIS F 197 PHE 0.019 0.002 PHE B 118 TYR 0.026 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 *********************** 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 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.937 Fit side-chains REVERT: B 33 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6629 (tm) REVERT: B 117 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7047 (ptm) REVERT: B 217 TYR cc_start: 0.7928 (m-80) cc_final: 0.7622 (m-80) REVERT: C 27 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7779 (mtt180) REVERT: C 139 ARG cc_start: 0.7644 (mtm180) cc_final: 0.7405 (mtm180) REVERT: C 222 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6810 (pmt) REVERT: C 308 ASP cc_start: 0.7394 (m-30) cc_final: 0.7165 (m-30) REVERT: E 206 SER cc_start: 0.8344 (t) cc_final: 0.8033 (m) REVERT: E 237 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7883 (mt) REVERT: F 208 ARG cc_start: 0.7926 (ptt-90) cc_final: 0.7545 (ptt180) REVERT: F 239 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7387 (t0) REVERT: F 250 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7473 (mtm-85) REVERT: F 329 HIS cc_start: 0.8241 (m-70) cc_final: 0.7966 (m-70) REVERT: F 352 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8008 (mp10) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 1.1865 time to fit residues: 254.5197 Evaluate side-chains 211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 THR 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 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 222 MET 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 E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET 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 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 56 optimal weight: 0.0270 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 142 GLN F 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135392 restraints weight = 11534.829| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.78 r_work: 0.3742 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8912 Z= 0.202 Angle : 0.557 9.398 12095 Z= 0.286 Chirality : 0.044 0.172 1373 Planarity : 0.004 0.041 1537 Dihedral : 4.623 30.113 1223 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.13 % Allowed : 20.24 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1108 helix: -0.00 (0.29), residues: 355 sheet: -0.09 (0.30), residues: 272 loop : -1.30 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.007 0.001 HIS F 197 PHE 0.018 0.002 PHE B 118 TYR 0.022 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 ********************** 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: 38 poor density : 184 time to evaluate : 0.917 Fit side-chains REVERT: B 33 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6549 (tm) REVERT: B 217 TYR cc_start: 0.7924 (m-80) cc_final: 0.7611 (m-80) REVERT: C 27 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7767 (mtt180) REVERT: C 83 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7901 (tppt) REVERT: C 139 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7430 (mtm180) REVERT: C 222 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6750 (pmt) REVERT: C 233 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: C 308 ASP cc_start: 0.7348 (m-30) cc_final: 0.7123 (m-30) REVERT: E 206 SER cc_start: 0.8344 (t) cc_final: 0.8039 (m) REVERT: E 237 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (mt) REVERT: F 239 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7446 (t0) REVERT: F 250 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: F 329 HIS cc_start: 0.8238 (m-70) cc_final: 0.7986 (m-70) REVERT: F 352 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7998 (mp10) outliers start: 38 outliers final: 23 residues processed: 208 average time/residue: 1.2088 time to fit residues: 269.3893 Evaluate side-chains 212 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain B residue 125 THR 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 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 202 ARG Chi-restraints excluded: chain C residue 222 MET 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 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 E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET 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 106 optimal weight: 0.2980 chunk 14 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 0.0030 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 109 GLN C 115 ASN C 345 ASN E 142 GLN F 246 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.151484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136522 restraints weight = 11560.880| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.78 r_work: 0.3753 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8912 Z= 0.174 Angle : 0.542 9.418 12095 Z= 0.279 Chirality : 0.043 0.167 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.508 28.447 1223 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.03 % Allowed : 20.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1108 helix: 0.07 (0.29), residues: 355 sheet: -0.06 (0.30), residues: 272 loop : -1.23 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.007 0.001 HIS F 197 PHE 0.025 0.001 PHE F 240 TYR 0.020 0.001 TYR E 235 ARG 0.008 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7847.00 seconds wall clock time: 138 minutes 45.10 seconds (8325.10 seconds total)