Starting phenix.real_space_refine on Fri Nov 15 11:29:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/11_2024/8jlj_36399_neut.cif" } resolution = 3.1 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= -0.002 sd= 0.120 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 63 5.16 5 C 5676 2.51 5 N 1525 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2147 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8918 At special positions: 0 Unit cell: (90.95, 125.8, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 63 16.00 O 1653 8.00 N 1525 7.00 C 5676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 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: 28 helices and 13 sheets defined 38.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.610A pdb=" N GLN A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.903A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.785A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.998A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.593A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.536A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'R' and resid 24 through 49 removed outlier: 4.023A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 86 removed outlier: 3.696A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 161 removed outlier: 3.849A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) Proline residue: R 150 - end of helix removed outlier: 3.642A pdb=" N TYR R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY R 156 " --> pdb=" O VAL R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 176 Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 198 through 225 removed outlier: 3.977A pdb=" N VAL R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET R 205 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 removed outlier: 3.805A pdb=" N GLY R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.528A pdb=" N THR R 268 " --> pdb=" O PHE R 264 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 297 removed outlier: 3.918A pdb=" N PHE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 292 " --> pdb=" O TRP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 302 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.500A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.941A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.544A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.711A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.851A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.644A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.761A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.161A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.925A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.580A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.065A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.861A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.067A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.533A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.984A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.618A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.726A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1137 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: 2.44 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 2902 1.36 - 1.54: 6050 1.54 - 1.73: 69 1.73 - 1.91: 93 1.91 - 2.10: 1 Bond restraints: 9115 Sorted by residual: bond pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 1.526 1.608 -0.082 1.37e-02 5.33e+03 3.59e+01 bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.453 1.530 -0.077 1.31e-02 5.83e+03 3.42e+01 bond pdb=" C VAL R 204 " pdb=" N MET R 205 " ideal model delta sigma weight residual 1.335 1.262 0.072 1.25e-02 6.40e+03 3.33e+01 bond pdb=" C SER R 79 " pdb=" O SER R 79 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.18e-02 7.18e+03 3.29e+01 bond pdb=" N MET R 205 " pdb=" CA MET R 205 " ideal model delta sigma weight residual 1.459 1.392 0.067 1.20e-02 6.94e+03 3.11e+01 ... (remaining 9110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11917 2.56 - 5.13: 340 5.13 - 7.69: 77 7.69 - 10.25: 8 10.25 - 12.82: 3 Bond angle restraints: 12345 Sorted by residual: angle pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 110.55 123.37 -12.82 1.35e+00 5.49e-01 9.01e+01 angle pdb=" N LEU A 360 " pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 114.12 103.86 10.26 1.39e+00 5.18e-01 5.45e+01 angle pdb=" N CYS R 260 " pdb=" CA CYS R 260 " pdb=" C CYS R 260 " ideal model delta sigma weight residual 113.01 121.35 -8.34 1.20e+00 6.94e-01 4.83e+01 angle pdb=" N THR R 83 " pdb=" CA THR R 83 " pdb=" C THR R 83 " ideal model delta sigma weight residual 111.28 104.31 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.28 104.50 6.78 1.09e+00 8.42e-01 3.87e+01 ... (remaining 12340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4936 17.85 - 35.69: 379 35.69 - 53.54: 64 53.54 - 71.38: 22 71.38 - 89.23: 7 Dihedral angle restraints: 5408 sinusoidal: 2121 harmonic: 3287 Sorted by residual: dihedral pdb=" C ASN R 40 " pdb=" N ASN R 40 " pdb=" CA ASN R 40 " pdb=" CB ASN R 40 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR A 33 " pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" CB THR A 33 " ideal model delta harmonic sigma weight residual -122.00 -134.42 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1181 0.077 - 0.155: 160 0.155 - 0.232: 28 0.232 - 0.310: 6 0.310 - 0.387: 3 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB VAL R 208 " pdb=" CA VAL R 208 " pdb=" CG1 VAL R 208 " pdb=" CG2 VAL R 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA THR A 33 " pdb=" N THR A 33 " pdb=" C THR A 33 " pdb=" CB THR A 33 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1375 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 20 " 0.024 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLU A 20 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU A 20 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS A 21 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 251 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C GLY R 251 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY R 251 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE R 252 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 293 " 0.022 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C ASN R 293 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN R 293 " 0.026 2.00e-02 2.50e+03 pdb=" N SER R 294 " 0.024 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.80: 2201 2.80 - 3.34: 8232 3.34 - 3.88: 14524 3.88 - 4.42: 17322 4.42 - 4.96: 30277 Nonbonded interactions: 72556 Sorted by model distance: nonbonded pdb=" OE1 GLU A 311 " pdb=" NH2 ARG A 314 " model vdw 2.256 3.120 nonbonded pdb=" ND2 ASN R 163 " pdb=" O PHE R 184 " model vdw 2.266 3.120 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.324 3.040 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.340 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.361 3.040 ... (remaining 72551 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.090 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.008 0.082 9115 Z= 0.519 Angle : 0.993 12.817 12345 Z= 0.679 Chirality : 0.059 0.387 1378 Planarity : 0.006 0.061 1565 Dihedral : 13.597 89.229 3281 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 3.09 % Favored : 96.08 % Cbeta Deviations : 0.28 % 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: -0.40 (0.26), residues: 1116 helix: -0.23 (0.28), residues: 376 sheet: 1.34 (0.35), residues: 262 loop : -1.19 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 147 HIS 0.011 0.001 HIS A 324 PHE 0.039 0.002 PHE R 304 TYR 0.018 0.001 TYR R 213 ARG 0.003 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8363 (pt0) cc_final: 0.8120 (pt0) REVERT: B 186 ASP cc_start: 0.7640 (p0) cc_final: 0.7245 (p0) REVERT: R 165 LYS cc_start: 0.6515 (mttm) cc_final: 0.6295 (ptmt) REVERT: R 195 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: S 7 SER cc_start: 0.7338 (t) cc_final: 0.7018 (p) REVERT: S 20 LEU cc_start: 0.7457 (mt) cc_final: 0.7238 (mp) REVERT: S 70 ILE cc_start: 0.8041 (pt) cc_final: 0.7616 (tt) REVERT: S 89 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6414 (mp0) outliers start: 8 outliers final: 4 residues processed: 174 average time/residue: 0.2796 time to fit residues: 63.2599 Evaluate side-chains 129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 197 HIS A 261 GLN B 75 GLN B 268 ASN B 293 ASN R 40 ASN S 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9115 Z= 0.216 Angle : 0.638 8.513 12345 Z= 0.335 Chirality : 0.045 0.230 1378 Planarity : 0.005 0.040 1565 Dihedral : 5.573 69.174 1254 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 8.45 % Favored : 90.10 % 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: 0.17 (0.26), residues: 1116 helix: 1.09 (0.28), residues: 382 sheet: 1.10 (0.35), residues: 258 loop : -1.29 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.008 0.002 HIS B 225 PHE 0.018 0.002 PHE A 189 TYR 0.022 0.002 TYR S 235 ARG 0.003 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.998 Fit side-chains REVERT: B 186 ASP cc_start: 0.7889 (p0) cc_final: 0.7016 (p0) REVERT: B 217 MET cc_start: 0.8110 (ppp) cc_final: 0.7458 (ppp) REVERT: R 81 VAL cc_start: 0.7488 (p) cc_final: 0.7252 (t) REVERT: R 133 LYS cc_start: 0.8231 (mttt) cc_final: 0.8015 (mttm) REVERT: R 165 LYS cc_start: 0.6658 (mttm) cc_final: 0.6356 (ptpt) REVERT: R 217 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7284 (mmtm) REVERT: S 70 ILE cc_start: 0.8027 (pt) cc_final: 0.7809 (tt) REVERT: S 89 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6679 (mp0) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.2592 time to fit residues: 50.0886 Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9115 Z= 0.133 Angle : 0.509 10.704 12345 Z= 0.267 Chirality : 0.041 0.142 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.105 75.435 1244 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.24 % Allowed : 11.44 % Favored : 87.32 % 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: 0.50 (0.26), residues: 1116 helix: 1.68 (0.28), residues: 382 sheet: 0.98 (0.33), residues: 277 loop : -1.30 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 235 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.966 Fit side-chains REVERT: B 186 ASP cc_start: 0.7809 (p0) cc_final: 0.6918 (p0) REVERT: B 217 MET cc_start: 0.8105 (ppp) cc_final: 0.7420 (ppp) REVERT: R 81 VAL cc_start: 0.7473 (p) cc_final: 0.7261 (t) REVERT: R 133 LYS cc_start: 0.8221 (mttt) cc_final: 0.7927 (mttm) REVERT: R 157 MET cc_start: 0.7715 (ttp) cc_final: 0.7456 (ttp) REVERT: R 165 LYS cc_start: 0.6701 (mttm) cc_final: 0.6369 (ptpt) REVERT: R 217 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7411 (tptt) REVERT: S 140 MET cc_start: 0.8573 (mmm) cc_final: 0.8241 (mmm) REVERT: S 160 ARG cc_start: 0.7376 (ttt180) cc_final: 0.7152 (ttp-170) outliers start: 12 outliers final: 6 residues processed: 137 average time/residue: 0.2668 time to fit residues: 48.1217 Evaluate side-chains 130 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain Y residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9115 Z= 0.153 Angle : 0.534 9.947 12345 Z= 0.282 Chirality : 0.042 0.140 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.238 78.948 1244 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.75 % Allowed : 11.65 % Favored : 86.60 % 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: 0.69 (0.26), residues: 1116 helix: 1.87 (0.28), residues: 384 sheet: 1.08 (0.32), residues: 285 loop : -1.28 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.014 0.001 PHE B 199 TYR 0.021 0.001 TYR S 235 ARG 0.003 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.026 Fit side-chains REVERT: B 186 ASP cc_start: 0.7941 (p0) cc_final: 0.7034 (p0) REVERT: B 217 MET cc_start: 0.8110 (ppp) cc_final: 0.7478 (ppp) REVERT: B 234 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.6639 (t80) REVERT: R 81 VAL cc_start: 0.7492 (p) cc_final: 0.7288 (t) REVERT: R 133 LYS cc_start: 0.8259 (mttt) cc_final: 0.7986 (mttm) REVERT: R 217 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7331 (mmtm) outliers start: 17 outliers final: 11 residues processed: 140 average time/residue: 0.2569 time to fit residues: 48.2105 Evaluate side-chains 140 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.0030 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9115 Z= 0.149 Angle : 0.522 8.167 12345 Z= 0.276 Chirality : 0.042 0.136 1378 Planarity : 0.004 0.036 1565 Dihedral : 5.274 81.388 1243 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.86 % Allowed : 12.99 % Favored : 85.15 % 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: 0.79 (0.26), residues: 1116 helix: 1.99 (0.28), residues: 383 sheet: 1.13 (0.32), residues: 287 loop : -1.25 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 232 PHE 0.013 0.001 PHE B 199 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.880 Fit side-chains REVERT: B 186 ASP cc_start: 0.7971 (p0) cc_final: 0.7112 (p0) REVERT: B 234 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.6650 (t80) REVERT: R 81 VAL cc_start: 0.7403 (p) cc_final: 0.7181 (t) REVERT: R 133 LYS cc_start: 0.8278 (mttt) cc_final: 0.7999 (mttm) REVERT: R 200 ILE cc_start: 0.8433 (mm) cc_final: 0.8065 (mt) REVERT: R 217 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7240 (mmtm) REVERT: S 7 SER cc_start: 0.7772 (t) cc_final: 0.7221 (p) REVERT: S 235 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5528 (t80) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.2412 time to fit residues: 46.1200 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0270 chunk 26 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9115 Z= 0.245 Angle : 0.619 10.342 12345 Z= 0.328 Chirality : 0.045 0.145 1378 Planarity : 0.005 0.046 1565 Dihedral : 5.777 86.415 1243 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.06 % Allowed : 14.02 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.61 (0.26), residues: 1116 helix: 1.77 (0.27), residues: 389 sheet: 1.18 (0.33), residues: 270 loop : -1.36 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.016 0.002 PHE B 151 TYR 0.032 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.955 Fit side-chains REVERT: A 277 ASP cc_start: 0.6668 (m-30) cc_final: 0.6400 (m-30) REVERT: B 234 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.6708 (t80) REVERT: R 81 VAL cc_start: 0.7372 (p) cc_final: 0.7165 (t) REVERT: R 200 ILE cc_start: 0.8507 (mm) cc_final: 0.8161 (mt) REVERT: R 217 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7151 (mmtm) REVERT: S 235 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.5723 (t80) outliers start: 20 outliers final: 12 residues processed: 146 average time/residue: 0.2672 time to fit residues: 51.5570 Evaluate side-chains 144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9115 Z= 0.139 Angle : 0.513 8.761 12345 Z= 0.272 Chirality : 0.042 0.138 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.512 84.898 1243 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.75 % Allowed : 14.64 % Favored : 83.61 % 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: 0.79 (0.26), residues: 1116 helix: 2.06 (0.28), residues: 383 sheet: 1.19 (0.32), residues: 285 loop : -1.36 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.017 0.001 TYR S 235 ARG 0.002 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.060 Fit side-chains REVERT: A 237 LEU cc_start: 0.8065 (mp) cc_final: 0.7826 (mm) REVERT: A 277 ASP cc_start: 0.6662 (m-30) cc_final: 0.6392 (m-30) REVERT: B 219 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7452 (mmm160) REVERT: B 234 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.6713 (t80) REVERT: R 81 VAL cc_start: 0.7264 (p) cc_final: 0.7054 (t) REVERT: R 119 ASP cc_start: 0.8606 (t70) cc_final: 0.8280 (t0) REVERT: R 200 ILE cc_start: 0.8491 (mm) cc_final: 0.8150 (mt) REVERT: R 217 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7189 (mmtm) REVERT: S 7 SER cc_start: 0.7799 (t) cc_final: 0.7239 (p) REVERT: S 235 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5700 (t80) outliers start: 17 outliers final: 14 residues processed: 145 average time/residue: 0.2388 time to fit residues: 46.7450 Evaluate side-chains 149 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9115 Z= 0.137 Angle : 0.511 9.544 12345 Z= 0.270 Chirality : 0.042 0.136 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.469 86.602 1243 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.86 % Allowed : 14.85 % Favored : 83.30 % 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: 0.86 (0.26), residues: 1116 helix: 2.13 (0.28), residues: 383 sheet: 1.19 (0.32), residues: 287 loop : -1.32 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR S 235 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.128 Fit side-chains REVERT: A 237 LEU cc_start: 0.8085 (mp) cc_final: 0.7806 (mm) REVERT: A 277 ASP cc_start: 0.6663 (m-30) cc_final: 0.6389 (m-30) REVERT: B 186 ASP cc_start: 0.8006 (p0) cc_final: 0.7236 (p0) REVERT: B 219 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7452 (mmm160) REVERT: B 234 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.6689 (t80) REVERT: R 81 VAL cc_start: 0.7226 (p) cc_final: 0.7018 (t) REVERT: R 200 ILE cc_start: 0.8491 (mm) cc_final: 0.8162 (mt) REVERT: R 217 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7195 (mmtm) REVERT: S 7 SER cc_start: 0.7796 (t) cc_final: 0.7290 (p) REVERT: S 235 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5727 (t80) outliers start: 18 outliers final: 15 residues processed: 141 average time/residue: 0.2398 time to fit residues: 45.8105 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 47 GLU 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: 4.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9115 Z= 0.131 Angle : 0.504 9.652 12345 Z= 0.266 Chirality : 0.041 0.137 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.455 87.539 1243 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.86 % Allowed : 15.26 % Favored : 82.89 % 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: 0.91 (0.26), residues: 1116 helix: 2.17 (0.28), residues: 383 sheet: 1.16 (0.32), residues: 289 loop : -1.26 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.016 0.001 TYR S 235 ARG 0.002 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.044 Fit side-chains REVERT: A 237 LEU cc_start: 0.8113 (mp) cc_final: 0.7824 (mm) REVERT: A 277 ASP cc_start: 0.6713 (m-30) cc_final: 0.6431 (m-30) REVERT: B 186 ASP cc_start: 0.7981 (p0) cc_final: 0.7212 (p0) REVERT: B 219 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7458 (mmm160) REVERT: B 234 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 259 GLN cc_start: 0.8085 (mt0) cc_final: 0.7873 (mt0) REVERT: R 200 ILE cc_start: 0.8483 (mm) cc_final: 0.8174 (mt) REVERT: R 217 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7165 (mmtm) REVERT: S 7 SER cc_start: 0.7799 (t) cc_final: 0.7280 (p) REVERT: S 235 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5719 (t80) outliers start: 18 outliers final: 15 residues processed: 141 average time/residue: 0.2280 time to fit residues: 43.9305 Evaluate side-chains 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.0060 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.0970 chunk 93 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 overall best weight: 0.2410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9115 Z= 0.107 Angle : 0.462 8.365 12345 Z= 0.242 Chirality : 0.040 0.126 1378 Planarity : 0.003 0.038 1565 Dihedral : 5.244 87.232 1243 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.13 % Allowed : 16.08 % Favored : 82.78 % 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: 1.06 (0.26), residues: 1116 helix: 2.32 (0.28), residues: 383 sheet: 1.14 (0.32), residues: 291 loop : -1.11 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR S 190 ARG 0.003 0.000 ARG R 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.060 Fit side-chains REVERT: A 277 ASP cc_start: 0.6630 (m-30) cc_final: 0.6359 (m-30) REVERT: B 186 ASP cc_start: 0.7717 (p0) cc_final: 0.6954 (p0) REVERT: B 219 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7464 (mmm160) REVERT: B 234 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.6626 (t80) REVERT: R 119 ASP cc_start: 0.8463 (t70) cc_final: 0.8242 (t0) REVERT: R 200 ILE cc_start: 0.8433 (mm) cc_final: 0.8167 (mt) REVERT: R 217 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7126 (mmtm) REVERT: S 7 SER cc_start: 0.7690 (t) cc_final: 0.7274 (p) outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.2355 time to fit residues: 44.2766 Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.154199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.117194 restraints weight = 7443.057| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.07 r_work: 0.2883 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9115 Z= 0.250 Angle : 0.617 11.569 12345 Z= 0.326 Chirality : 0.045 0.147 1378 Planarity : 0.004 0.046 1565 Dihedral : 5.825 89.279 1243 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.44 % Allowed : 15.67 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.73 (0.26), residues: 1116 helix: 1.91 (0.28), residues: 389 sheet: 1.07 (0.32), residues: 277 loop : -1.24 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 261 HIS 0.006 0.002 HIS S 232 PHE 0.016 0.002 PHE B 151 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG R 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.95 seconds wall clock time: 43 minutes 40.87 seconds (2620.87 seconds total)