Starting phenix.real_space_refine on Sat Dec 28 14:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xwo_33497/12_2024/7xwo_33497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xwo_33497/12_2024/7xwo_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_33497/12_2024/7xwo_33497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xwo_33497/12_2024/7xwo_33497.map" model { file = "/net/cci-nas-00/data/ceres_data/7xwo_33497/12_2024/7xwo_33497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xwo_33497/12_2024/7xwo_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-5532/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: 5.86, per 1000 atoms: 0.67 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 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: 1.04 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: 2.45 Time building geometry restraints manager: 2.55 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: 1.910 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.790 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- 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 : 1.425 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: 1.1502 time to fit residues: 265.6428 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 : 0.978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.4827 (mmm) cc_final: 0.4489 (mmm) REVERT: B 117 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6419 (ptm) REVERT: B 136 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7560 (t) REVERT: C 193 MET cc_start: 0.7964 (mmm) cc_final: 0.7619 (mmm) REVERT: C 308 ASP cc_start: 0.6875 (m-30) cc_final: 0.6654 (m-30) REVERT: F 262 ASP cc_start: 0.7128 (p0) cc_final: 0.6800 (p0) REVERT: F 276 GLU cc_start: 0.6663 (pm20) cc_final: 0.6345 (pm20) outliers start: 27 outliers final: 8 residues processed: 209 average time/residue: 1.2654 time to fit residues: 281.1680 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 : 1.019 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.0020 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1929 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= 0.182 Angle : 0.537 6.688 12095 Z= 0.286 Chirality : 0.043 0.205 1373 Planarity : 0.004 0.049 1537 Dihedral : 5.059 34.560 1224 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.81 % Allowed : 15.89 % Favored : 80.30 % 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: -2.34 (0.23), residues: 1108 helix: -1.79 (0.25), residues: 348 sheet: -0.46 (0.30), residues: 280 loop : -1.95 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.007 0.001 HIS F 197 PHE 0.023 0.002 PHE B 118 TYR 0.027 0.001 TYR E 235 ARG 0.008 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 226 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6413 (ptm) REVERT: B 136 VAL cc_start: 0.7766 (OUTLIER) cc_final: 0.7555 (t) REVERT: B 217 TYR cc_start: 0.7782 (m-80) cc_final: 0.7420 (m-80) REVERT: C 79 SER cc_start: 0.7707 (p) cc_final: 0.7493 (p) REVERT: C 193 MET cc_start: 0.7922 (mmm) cc_final: 0.7688 (mmm) REVERT: C 217 ASP cc_start: 0.7507 (t0) cc_final: 0.7293 (t0) REVERT: C 224 ARG cc_start: 0.7000 (ptp90) cc_final: 0.6411 (ptp90) REVERT: C 233 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: C 332 VAL cc_start: 0.7864 (t) cc_final: 0.7637 (t) REVERT: E 85 LEU cc_start: 0.8714 (mt) cc_final: 0.8510 (mm) REVERT: E 206 SER cc_start: 0.8009 (t) cc_final: 0.7781 (m) REVERT: F 238 ASN cc_start: 0.8060 (m110) cc_final: 0.7767 (m110) REVERT: F 329 HIS cc_start: 0.8040 (m-70) cc_final: 0.7830 (m-70) outliers start: 35 outliers final: 13 residues processed: 211 average time/residue: 1.2394 time to fit residues: 278.3089 Evaluate side-chains 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain 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 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 311 GLU 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 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 0.0060 chunk 48 optimal weight: 0.0030 chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.2406 ------------------------------------------------------------------------------- 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 F 259 ASN F 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8912 Z= 0.144 Angle : 0.518 7.559 12095 Z= 0.271 Chirality : 0.042 0.181 1373 Planarity : 0.004 0.046 1537 Dihedral : 4.653 28.713 1224 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.59 % Allowed : 17.19 % Favored : 79.22 % 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: -1.77 (0.24), residues: 1108 helix: -1.08 (0.27), residues: 352 sheet: -0.22 (0.30), residues: 278 loop : -1.75 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.009 0.001 HIS F 197 PHE 0.024 0.001 PHE B 118 TYR 0.025 0.001 TYR E 235 ARG 0.007 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 236 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.943 Fit side-chains REVERT: B 117 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6383 (ptm) REVERT: B 136 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7538 (t) REVERT: B 206 TYR cc_start: 0.7416 (t80) cc_final: 0.7116 (t80) REVERT: B 217 TYR cc_start: 0.7737 (m-80) cc_final: 0.7372 (m-80) REVERT: B 261 ILE cc_start: 0.7498 (pt) cc_final: 0.7290 (mp) REVERT: C 81 ASP cc_start: 0.7247 (p0) cc_final: 0.6995 (p0) REVERT: C 122 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7447 (mt) REVERT: C 139 ARG cc_start: 0.6619 (mtm180) cc_final: 0.6411 (mtm180) REVERT: C 193 MET cc_start: 0.7921 (mmm) cc_final: 0.7692 (mmm) REVERT: C 233 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: F 208 ARG cc_start: 0.7593 (ptt180) cc_final: 0.7283 (ptt-90) REVERT: F 239 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6683 (t0) REVERT: F 250 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6638 (mtm-85) REVERT: F 352 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7381 (mp10) outliers start: 33 outliers final: 11 residues processed: 219 average time/residue: 1.1867 time to fit residues: 277.0916 Evaluate side-chains 212 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 257 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.004 0.033 8912 Z= 0.247 Angle : 0.564 7.743 12095 Z= 0.295 Chirality : 0.044 0.218 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.903 34.029 1224 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.24 % Allowed : 18.72 % Favored : 77.04 % 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: -1.58 (0.24), residues: 1108 helix: -0.82 (0.28), residues: 351 sheet: -0.26 (0.31), residues: 271 loop : -1.60 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 216 HIS 0.012 0.001 HIS B 282 PHE 0.023 0.002 PHE B 118 TYR 0.030 0.002 TYR E 235 ARG 0.008 0.001 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: 39 poor density : 189 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6679 (tm) REVERT: B 117 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6329 (ptm) REVERT: C 122 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7800 (mt) REVERT: C 139 ARG cc_start: 0.6694 (mtm180) cc_final: 0.6478 (mtm180) REVERT: C 193 MET cc_start: 0.7959 (mmm) cc_final: 0.7660 (mmm) REVERT: F 239 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6732 (t0) REVERT: F 329 HIS cc_start: 0.8012 (m-70) cc_final: 0.7757 (m-70) REVERT: F 352 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7399 (mp10) outliers start: 39 outliers final: 17 residues processed: 209 average time/residue: 1.2671 time to fit residues: 281.5132 Evaluate side-chains 212 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET 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 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 336 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.0020 overall best weight: 0.3946 ------------------------------------------------------------------------------- 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 E 142 GLN F 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2534 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= 0.173 Angle : 0.532 7.333 12095 Z= 0.277 Chirality : 0.043 0.192 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.608 29.484 1223 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.13 % Allowed : 19.48 % 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: -1.29 (0.24), residues: 1108 helix: -0.51 (0.29), residues: 350 sheet: -0.09 (0.30), residues: 272 loop : -1.48 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 68 HIS 0.008 0.001 HIS F 197 PHE 0.020 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 226 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6558 (tm) REVERT: B 117 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6386 (ptm) REVERT: B 217 TYR cc_start: 0.7747 (m-80) cc_final: 0.7388 (m-80) REVERT: B 261 ILE cc_start: 0.7518 (pt) cc_final: 0.7310 (mp) REVERT: C 122 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7697 (mt) REVERT: C 139 ARG cc_start: 0.6662 (mtm180) cc_final: 0.6448 (mtm180) REVERT: C 193 MET cc_start: 0.7946 (mmm) cc_final: 0.7680 (mmm) REVERT: C 326 THR cc_start: 0.7552 (p) cc_final: 0.6961 (t) REVERT: C 332 VAL cc_start: 0.7781 (t) cc_final: 0.7550 (t) REVERT: F 239 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6670 (t0) REVERT: F 329 HIS cc_start: 0.7924 (m-70) cc_final: 0.7650 (m-70) REVERT: F 352 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7434 (mp10) outliers start: 38 outliers final: 19 residues processed: 210 average time/residue: 1.1596 time to fit residues: 260.7745 Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain B residue 207 PHE 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 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 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 64 LYS 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 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 78 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 E 142 GLN F 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8912 Z= 0.214 Angle : 0.562 9.447 12095 Z= 0.289 Chirality : 0.043 0.201 1373 Planarity : 0.004 0.041 1537 Dihedral : 4.701 32.362 1223 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.22 % Allowed : 19.26 % Favored : 75.52 % 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: -1.17 (0.25), residues: 1108 helix: -0.37 (0.29), residues: 350 sheet: -0.09 (0.30), residues: 272 loop : -1.41 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 174 HIS 0.006 0.001 HIS F 197 PHE 0.021 0.002 PHE F 240 TYR 0.028 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 229 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.887 Fit side-chains REVERT: B 33 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6539 (tm) REVERT: B 245 MET cc_start: 0.6815 (ppp) cc_final: 0.6580 (tmt) REVERT: B 261 ILE cc_start: 0.7573 (pt) cc_final: 0.7354 (mp) REVERT: C 24 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6976 (ttp-110) REVERT: C 47 ARG cc_start: 0.6397 (tpt90) cc_final: 0.6160 (tpt90) REVERT: C 122 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7716 (mt) REVERT: C 193 MET cc_start: 0.7942 (mmm) cc_final: 0.7668 (mmm) REVERT: C 326 THR cc_start: 0.7609 (p) cc_final: 0.6891 (t) REVERT: C 332 VAL cc_start: 0.7803 (t) cc_final: 0.7577 (t) REVERT: F 230 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: F 239 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6648 (t0) REVERT: F 250 ARG cc_start: 0.6863 (mtm-85) cc_final: 0.6627 (mtm-85) REVERT: F 300 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6853 (mtm180) REVERT: F 329 HIS cc_start: 0.7948 (m-70) cc_final: 0.7660 (m-70) REVERT: F 352 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7494 (mp10) outliers start: 48 outliers final: 27 residues processed: 206 average time/residue: 1.2106 time to fit residues: 266.0594 Evaluate side-chains 221 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 109 GLN 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 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 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 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 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 142 GLN F 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8912 Z= 0.242 Angle : 0.569 8.623 12095 Z= 0.294 Chirality : 0.044 0.212 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.784 32.036 1223 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.01 % Allowed : 19.37 % 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: -1.08 (0.25), residues: 1108 helix: -0.23 (0.29), residues: 353 sheet: -0.09 (0.30), residues: 274 loop : -1.40 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 174 HIS 0.009 0.001 HIS F 197 PHE 0.020 0.002 PHE F 240 TYR 0.028 0.002 TYR E 235 ARG 0.009 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 237 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6577 (tm) REVERT: F 230 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: F 239 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6707 (t0) REVERT: F 250 ARG cc_start: 0.6866 (mtm-85) cc_final: 0.6626 (mtm-85) REVERT: F 329 HIS cc_start: 0.7966 (m-70) cc_final: 0.7687 (m-70) REVERT: F 352 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7488 (mp10) outliers start: 46 outliers final: 27 residues processed: 217 average time/residue: 1.2052 time to fit residues: 278.6548 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 109 GLN 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 224 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 282 HIS 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 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 328 ASP 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 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 246 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 E 142 GLN F 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2606 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= 0.233 Angle : 0.566 8.741 12095 Z= 0.293 Chirality : 0.044 0.187 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.769 32.112 1223 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.46 % Allowed : 20.13 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -1.02 (0.25), residues: 1108 helix: -0.19 (0.29), residues: 354 sheet: -0.07 (0.30), residues: 274 loop : -1.33 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 174 HIS 0.009 0.001 HIS F 197 PHE 0.020 0.002 PHE F 240 TYR 0.022 0.002 TYR E 235 ARG 0.009 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 230 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.001 Fit side-chains REVERT: B 33 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6525 (tm) REVERT: B 217 TYR cc_start: 0.7774 (m-80) cc_final: 0.7466 (m-80) REVERT: C 193 MET cc_start: 0.7922 (mmm) cc_final: 0.7640 (mmm) REVERT: F 230 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: F 239 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6727 (t0) REVERT: F 250 ARG cc_start: 0.6858 (mtm-85) cc_final: 0.6632 (mtm-85) REVERT: F 329 HIS cc_start: 0.7972 (m-70) cc_final: 0.7692 (m-70) REVERT: F 352 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7489 (mp10) outliers start: 41 outliers final: 29 residues processed: 211 average time/residue: 1.2277 time to fit residues: 275.4316 Evaluate side-chains 227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 109 GLN 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 224 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 233 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain 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 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 E 142 GLN F 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8912 Z= 0.265 Angle : 0.586 8.935 12095 Z= 0.301 Chirality : 0.045 0.194 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.817 32.772 1223 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -1.00 (0.25), residues: 1108 helix: -0.15 (0.29), residues: 354 sheet: -0.07 (0.30), residues: 274 loop : -1.34 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 216 HIS 0.011 0.001 HIS B 282 PHE 0.019 0.002 PHE F 240 TYR 0.022 0.002 TYR E 235 ARG 0.009 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 226 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6492 (tm) REVERT: F 230 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: F 239 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6731 (t0) REVERT: F 250 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6639 (mtm-85) REVERT: F 329 HIS cc_start: 0.7995 (m-70) cc_final: 0.7705 (m-70) REVERT: F 352 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7517 (mp10) outliers start: 38 outliers final: 25 residues processed: 209 average time/residue: 1.2556 time to fit residues: 278.7160 Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 109 GLN 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 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 328 ASP 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 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.0040 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135691 restraints weight = 11459.655| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.77 r_work: 0.3747 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2718 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= 0.191 Angle : 0.563 9.764 12095 Z= 0.288 Chirality : 0.044 0.179 1373 Planarity : 0.004 0.041 1537 Dihedral : 4.660 30.219 1223 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.26 % Allowed : 21.22 % Favored : 75.52 % 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: -0.85 (0.25), residues: 1108 helix: 0.01 (0.29), residues: 354 sheet: -0.01 (0.30), residues: 272 loop : -1.25 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.008 0.001 HIS F 197 PHE 0.018 0.002 PHE F 240 TYR 0.022 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.25 seconds wall clock time: 81 minutes 21.54 seconds (4881.54 seconds total)