Starting phenix.real_space_refine on Sat Aug 23 05:58:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsc_34993/08_2025/8hsc_34993.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 70 5.16 5 C 6469 2.51 5 N 1751 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10180 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 747 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2008 Classifications: {'peptide': 273} Incomplete info: {'n_c_alpha_c_only': 11, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.66, per 1000 atoms: 0.26 Number of scatterers: 10180 At special positions: 0 Unit cell: (92.352, 121.472, 158.912, 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 70 16.00 O 1890 8.00 N 1751 7.00 C 6469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 309 " - pdb=" SG CYS E 374 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 327.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 19 sheets defined 31.7% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.659A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.162A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.579A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.897A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.514A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'F' and resid 47 through 51 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.947A pdb=" N GLU R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 49 removed outlier: 4.294A pdb=" N THR R 48 " --> pdb=" O GLU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 4.346A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.291A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA R 111 " --> pdb=" O PRO R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 130 through 133 removed outlier: 3.686A pdb=" N ASN R 133 " --> pdb=" O TYR R 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 138 through 153 Processing helix chain 'R' and resid 162 through 183 removed outlier: 4.370A pdb=" N CYS R 166 " --> pdb=" O ARG R 162 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY R 179 " --> pdb=" O TRP R 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 180 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.815A pdb=" N THR R 201 " --> pdb=" O VAL R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 223 removed outlier: 3.561A pdb=" N ARG R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 254 removed outlier: 3.870A pdb=" N MET R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 264 removed outlier: 3.812A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 282 removed outlier: 3.716A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.733A pdb=" N ASN R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 311 removed outlier: 3.906A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL R 308 " --> pdb=" O PHE R 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.145A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.156A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.990A pdb=" N LEU E 297 " --> pdb=" O GLU E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 330 through 334 removed outlier: 5.095A pdb=" N LEU E 332 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN E 323 " --> pdb=" O LEU E 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.616A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.753A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.062A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.737A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.520A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.136A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.939A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE F 53 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR F 131 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AC1, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.734A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2587 1.33 - 1.46: 3257 1.46 - 1.60: 4449 1.60 - 1.73: 0 1.73 - 1.86: 98 Bond restraints: 10391 Sorted by residual: bond pdb=" CG ASN R 94 " pdb=" OD1 ASN R 94 " ideal model delta sigma weight residual 1.231 1.199 0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 1.808 1.861 -0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" C THR R 86 " pdb=" N PRO R 87 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CG ASN R 94 " pdb=" ND2 ASN R 94 " ideal model delta sigma weight residual 1.328 1.297 0.031 2.10e-02 2.27e+03 2.18e+00 bond pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 ... (remaining 10386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 13761 2.06 - 4.11: 278 4.11 - 6.17: 36 6.17 - 8.22: 9 8.22 - 10.28: 4 Bond angle restraints: 14088 Sorted by residual: angle pdb=" C LYS S 76 " pdb=" N ASN S 77 " pdb=" CA ASN S 77 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA CYS R 119 " pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 angle pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " pdb=" NE ARG C 62 " ideal model delta sigma weight residual 112.00 119.76 -7.76 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CB MET C 21 " pdb=" CG MET C 21 " pdb=" SD MET C 21 " ideal model delta sigma weight residual 112.70 122.98 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA GLN E 375 " pdb=" CB GLN E 375 " pdb=" CG GLN E 375 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5142 17.94 - 35.88: 732 35.88 - 53.82: 197 53.82 - 71.75: 42 71.75 - 89.69: 13 Dihedral angle restraints: 6126 sinusoidal: 2271 harmonic: 3855 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASN R 133 " pdb=" C ASN R 133 " pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ARG R 117 " pdb=" C ARG R 117 " pdb=" N GLY R 118 " pdb=" CA GLY R 118 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1334 0.057 - 0.115: 245 0.115 - 0.172: 26 0.172 - 0.229: 8 0.229 - 0.287: 1 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR R 98 " pdb=" CA THR R 98 " pdb=" OG1 THR R 98 " pdb=" CG2 THR R 98 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU R 132 " pdb=" CB LEU R 132 " pdb=" CD1 LEU R 132 " pdb=" CD2 LEU R 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1611 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 86 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO R 87 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 87 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 87 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 140 " -0.023 2.00e-02 2.50e+03 1.77e-02 5.50e+00 pdb=" CG PHE R 140 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE R 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE R 140 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE R 140 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE R 140 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 140 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 173 " 0.010 2.00e-02 2.50e+03 1.51e-02 3.97e+00 pdb=" CG PHE R 173 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 173 " -0.000 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 400 2.71 - 3.26: 9543 3.26 - 3.80: 16632 3.80 - 4.35: 20168 4.35 - 4.90: 35260 Nonbonded interactions: 82003 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.247 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.264 3.040 ... (remaining 81998 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.003 0.053 10396 Z= 0.156 Angle : 0.698 10.276 14098 Z= 0.366 Chirality : 0.047 0.287 1614 Planarity : 0.005 0.067 1783 Dihedral : 18.311 89.693 3639 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.47 % Allowed : 36.23 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.23), residues: 1323 helix: -0.69 (0.26), residues: 361 sheet: -0.45 (0.26), residues: 390 loop : -1.08 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 168 TYR 0.024 0.002 TYR A 302 PHE 0.034 0.002 PHE R 173 TRP 0.027 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00347 (10391) covalent geometry : angle 0.69551 (14088) SS BOND : bond 0.00414 ( 5) SS BOND : angle 2.28271 ( 10) hydrogen bonds : bond 0.16932 ( 456) hydrogen bonds : angle 7.21568 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8579 (tpp) cc_final: 0.8376 (tpp) REVERT: A 261 ASP cc_start: 0.8820 (p0) cc_final: 0.8584 (p0) REVERT: B 59 TYR cc_start: 0.8919 (m-80) cc_final: 0.8716 (m-80) REVERT: S 208 GLU cc_start: 0.8087 (mp0) cc_final: 0.7696 (mp0) outliers start: 5 outliers final: 3 residues processed: 173 average time/residue: 0.0944 time to fit residues: 23.2048 Evaluate side-chains 173 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain S residue 74 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN C 11 GLN R 133 ASN R 272 HIS R 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106664 restraints weight = 14527.425| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.11 r_work: 0.3292 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10396 Z= 0.318 Angle : 0.676 7.001 14098 Z= 0.364 Chirality : 0.046 0.194 1614 Planarity : 0.005 0.056 1783 Dihedral : 5.267 54.776 1451 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 7.75 % Allowed : 30.25 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.23), residues: 1323 helix: -0.03 (0.27), residues: 373 sheet: -0.71 (0.25), residues: 402 loop : -1.17 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 236 TYR 0.028 0.002 TYR S 223 PHE 0.018 0.002 PHE B 241 TRP 0.016 0.002 TRP B 297 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00740 (10391) covalent geometry : angle 0.67489 (14088) SS BOND : bond 0.00226 ( 5) SS BOND : angle 1.54180 ( 10) hydrogen bonds : bond 0.04103 ( 456) hydrogen bonds : angle 5.42879 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 179 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 306 GLN cc_start: 0.8248 (tt0) cc_final: 0.7944 (tt0) REVERT: B 59 TYR cc_start: 0.9082 (m-80) cc_final: 0.8714 (m-80) REVERT: B 234 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: F 58 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6751 (tm-30) REVERT: F 117 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.6855 (ttp80) REVERT: R 78 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6983 (t80) REVERT: R 175 TRP cc_start: 0.7177 (m100) cc_final: 0.6853 (m100) REVERT: S 72 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6724 (ptm-80) REVERT: S 74 ASP cc_start: 0.8751 (m-30) cc_final: 0.8128 (m-30) REVERT: S 219 GLN cc_start: 0.7918 (pp30) cc_final: 0.7569 (pp30) REVERT: S 221 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8193 (tt) outliers start: 83 outliers final: 46 residues processed: 236 average time/residue: 0.0862 time to fit residues: 28.6730 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 241 GLN Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN R 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.168448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115197 restraints weight = 14398.128| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.12 r_work: 0.3445 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10396 Z= 0.121 Angle : 0.538 6.708 14098 Z= 0.286 Chirality : 0.041 0.165 1614 Planarity : 0.004 0.053 1783 Dihedral : 4.634 44.443 1449 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.01 % Allowed : 34.08 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.24), residues: 1323 helix: 0.46 (0.28), residues: 374 sheet: -0.38 (0.26), residues: 377 loop : -1.11 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.016 0.001 TYR S 178 PHE 0.011 0.001 PHE R 78 TRP 0.016 0.001 TRP R 267 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00267 (10391) covalent geometry : angle 0.53727 (14088) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.34526 ( 10) hydrogen bonds : bond 0.02993 ( 456) hydrogen bonds : angle 4.84225 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8270 (m-80) cc_final: 0.7823 (m-80) REVERT: B 45 MET cc_start: 0.8428 (mtp) cc_final: 0.7859 (mtt) REVERT: C 58 GLU cc_start: 0.8613 (pm20) cc_final: 0.8215 (pm20) REVERT: F 58 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6897 (tm-30) REVERT: F 117 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.6918 (ttp80) REVERT: R 78 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7018 (t80) REVERT: R 175 TRP cc_start: 0.7162 (m100) cc_final: 0.6914 (m100) REVERT: S 72 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6648 (ptm-80) REVERT: S 74 ASP cc_start: 0.8787 (m-30) cc_final: 0.8075 (m-30) outliers start: 43 outliers final: 25 residues processed: 208 average time/residue: 0.0828 time to fit residues: 24.1769 Evaluate side-chains 201 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 99 optimal weight: 0.3980 chunk 80 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 376 GLN A 306 GLN C 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108761 restraints weight = 14508.073| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.12 r_work: 0.3324 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10396 Z= 0.212 Angle : 0.587 7.142 14098 Z= 0.313 Chirality : 0.043 0.193 1614 Planarity : 0.004 0.050 1783 Dihedral : 4.709 43.430 1448 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.44 % Allowed : 31.37 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1323 helix: 0.60 (0.28), residues: 374 sheet: -0.59 (0.25), residues: 384 loop : -1.14 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.023 0.002 TYR S 223 PHE 0.016 0.002 PHE R 110 TRP 0.025 0.002 TRP R 267 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00496 (10391) covalent geometry : angle 0.58614 (14088) SS BOND : bond 0.00174 ( 5) SS BOND : angle 1.39356 ( 10) hydrogen bonds : bond 0.03228 ( 456) hydrogen bonds : angle 4.85571 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 298 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: A 302 TYR cc_start: 0.8687 (t80) cc_final: 0.8433 (t80) REVERT: B 45 MET cc_start: 0.8656 (mtp) cc_final: 0.8161 (mtt) REVERT: B 234 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: C 58 GLU cc_start: 0.8619 (pm20) cc_final: 0.8154 (pm20) REVERT: F 42 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7537 (ptpp) REVERT: F 58 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6799 (tm-30) REVERT: F 117 ARG cc_start: 0.7558 (ttp-170) cc_final: 0.6678 (ttp80) REVERT: R 78 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6968 (t80) REVERT: R 175 TRP cc_start: 0.7175 (m100) cc_final: 0.6885 (m100) REVERT: S 43 LYS cc_start: 0.8380 (mppt) cc_final: 0.8080 (mmmm) REVERT: S 72 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6548 (ptm-80) REVERT: S 74 ASP cc_start: 0.8837 (m-30) cc_final: 0.8240 (m-30) REVERT: S 113 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8336 (tp-100) outliers start: 69 outliers final: 43 residues processed: 224 average time/residue: 0.0894 time to fit residues: 28.3111 Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111577 restraints weight = 14393.138| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.11 r_work: 0.3359 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10396 Z= 0.141 Angle : 0.551 7.151 14098 Z= 0.293 Chirality : 0.042 0.171 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.535 42.392 1448 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.51 % Allowed : 32.59 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1323 helix: 0.81 (0.29), residues: 366 sheet: -0.39 (0.26), residues: 374 loop : -1.15 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.018 0.001 TYR S 223 PHE 0.013 0.001 PHE R 110 TRP 0.032 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (10391) covalent geometry : angle 0.55036 (14088) SS BOND : bond 0.00109 ( 5) SS BOND : angle 1.34447 ( 10) hydrogen bonds : bond 0.02903 ( 456) hydrogen bonds : angle 4.70477 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6026 (mm110) cc_final: 0.5810 (mm110) REVERT: A 298 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 314 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: B 45 MET cc_start: 0.8677 (mtp) cc_final: 0.8351 (mtt) REVERT: B 234 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 338 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 47 GLU cc_start: 0.8579 (pm20) cc_final: 0.8277 (pm20) REVERT: F 42 LYS cc_start: 0.7950 (ptmt) cc_final: 0.7525 (ptpp) REVERT: F 58 GLN cc_start: 0.7024 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 117 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.6633 (ttp80) REVERT: R 78 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6949 (t80) REVERT: R 175 TRP cc_start: 0.7134 (m100) cc_final: 0.6882 (m100) REVERT: S 43 LYS cc_start: 0.8310 (mppt) cc_final: 0.8006 (mmmm) REVERT: S 72 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6643 (ptm-80) REVERT: S 219 GLN cc_start: 0.7753 (pp30) cc_final: 0.7372 (pp30) outliers start: 59 outliers final: 41 residues processed: 232 average time/residue: 0.0866 time to fit residues: 28.5594 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110162 restraints weight = 14552.943| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.11 r_work: 0.3337 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10396 Z= 0.185 Angle : 0.594 12.183 14098 Z= 0.313 Chirality : 0.043 0.161 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.610 42.844 1448 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 6.54 % Allowed : 31.84 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.24), residues: 1323 helix: 0.79 (0.29), residues: 367 sheet: -0.48 (0.26), residues: 377 loop : -1.15 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 117 TYR 0.021 0.002 TYR S 223 PHE 0.017 0.002 PHE R 173 TRP 0.033 0.002 TRP R 267 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00434 (10391) covalent geometry : angle 0.58629 (14088) SS BOND : bond 0.00277 ( 5) SS BOND : angle 3.69044 ( 10) hydrogen bonds : bond 0.03003 ( 456) hydrogen bonds : angle 4.71168 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: A 298 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 314 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: B 45 MET cc_start: 0.8701 (mtp) cc_final: 0.8403 (mtt) REVERT: B 234 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 318 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 338 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 47 GLU cc_start: 0.8619 (pm20) cc_final: 0.8323 (pm20) REVERT: F 42 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7515 (ptpp) REVERT: F 117 ARG cc_start: 0.7393 (ttp-170) cc_final: 0.6587 (ttp80) REVERT: R 57 MET cc_start: 0.8206 (mmm) cc_final: 0.7981 (mmm) REVERT: R 78 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6987 (t80) REVERT: R 120 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7174 (tt) REVERT: R 175 TRP cc_start: 0.7130 (m100) cc_final: 0.6893 (m100) REVERT: S 43 LYS cc_start: 0.8343 (mppt) cc_final: 0.8041 (mmmm) REVERT: S 72 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6406 (ptm-80) REVERT: S 113 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8311 (tp-100) REVERT: S 219 GLN cc_start: 0.7769 (pp30) cc_final: 0.7324 (pp30) outliers start: 70 outliers final: 50 residues processed: 235 average time/residue: 0.0806 time to fit residues: 26.9385 Evaluate side-chains 233 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108899 restraints weight = 14459.703| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.11 r_work: 0.3323 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10396 Z= 0.216 Angle : 0.597 7.959 14098 Z= 0.317 Chirality : 0.044 0.168 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.709 42.963 1448 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 7.10 % Allowed : 31.75 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.23), residues: 1323 helix: 0.64 (0.28), residues: 373 sheet: -0.53 (0.26), residues: 382 loop : -1.17 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.024 0.002 TYR S 223 PHE 0.020 0.002 PHE R 140 TRP 0.033 0.002 TRP R 267 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00507 (10391) covalent geometry : angle 0.59605 (14088) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.44974 ( 10) hydrogen bonds : bond 0.03131 ( 456) hydrogen bonds : angle 4.77968 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: E 375 GLN cc_start: 0.5901 (mm110) cc_final: 0.5646 (mm110) REVERT: A 14 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 184 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 298 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: A 314 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7883 (mtpt) REVERT: B 45 MET cc_start: 0.8742 (mtp) cc_final: 0.8489 (mtt) REVERT: B 59 TYR cc_start: 0.9044 (m-80) cc_final: 0.8842 (m-80) REVERT: B 234 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 318 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 338 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 47 GLU cc_start: 0.8705 (pm20) cc_final: 0.8416 (pm20) REVERT: F 42 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7550 (ptpp) REVERT: F 117 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.6587 (ttp80) REVERT: R 78 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6960 (t80) REVERT: S 43 LYS cc_start: 0.8356 (mppt) cc_final: 0.8048 (mmmm) REVERT: S 113 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8313 (tp-100) outliers start: 76 outliers final: 58 residues processed: 238 average time/residue: 0.0838 time to fit residues: 28.7219 Evaluate side-chains 247 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.168684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118465 restraints weight = 13943.430| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.87 r_work: 0.3478 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10396 Z= 0.114 Angle : 0.560 9.011 14098 Z= 0.293 Chirality : 0.042 0.161 1614 Planarity : 0.004 0.046 1783 Dihedral : 4.448 42.592 1448 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.32 % Allowed : 33.24 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.24), residues: 1323 helix: 0.77 (0.28), residues: 366 sheet: -0.29 (0.27), residues: 369 loop : -1.11 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.030 0.001 TYR A 302 PHE 0.020 0.001 PHE R 173 TRP 0.036 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00258 (10391) covalent geometry : angle 0.55905 (14088) SS BOND : bond 0.00164 ( 5) SS BOND : angle 1.49048 ( 10) hydrogen bonds : bond 0.02814 ( 456) hydrogen bonds : angle 4.62931 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: A 314 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7916 (mtpt) REVERT: B 45 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8459 (mtt) REVERT: B 130 GLU cc_start: 0.8979 (mp0) cc_final: 0.8726 (mp0) REVERT: B 234 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: B 338 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8389 (mp) REVERT: F 42 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7550 (ptpp) REVERT: F 117 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.6759 (ttp80) REVERT: R 57 MET cc_start: 0.8190 (mmm) cc_final: 0.7970 (mmm) REVERT: R 78 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6970 (t80) REVERT: S 43 LYS cc_start: 0.8292 (mppt) cc_final: 0.7994 (mmmm) outliers start: 57 outliers final: 44 residues processed: 224 average time/residue: 0.0919 time to fit residues: 29.1652 Evaluate side-chains 232 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 6 optimal weight: 9.9990 chunk 106 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.167951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117107 restraints weight = 14125.169| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.91 r_work: 0.3468 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10396 Z= 0.130 Angle : 0.571 10.514 14098 Z= 0.297 Chirality : 0.042 0.182 1614 Planarity : 0.004 0.044 1783 Dihedral : 4.408 43.045 1448 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.32 % Allowed : 33.52 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.24), residues: 1323 helix: 0.78 (0.28), residues: 367 sheet: -0.33 (0.26), residues: 384 loop : -1.02 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.025 0.001 TYR A 302 PHE 0.019 0.001 PHE R 64 TRP 0.034 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00303 (10391) covalent geometry : angle 0.56911 (14088) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.96374 ( 10) hydrogen bonds : bond 0.02822 ( 456) hydrogen bonds : angle 4.58614 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.5672 (mm110) cc_final: 0.5286 (mt0) REVERT: A 298 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: A 314 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: B 130 GLU cc_start: 0.8965 (mp0) cc_final: 0.8700 (mp0) REVERT: B 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: B 338 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8349 (mp) REVERT: F 42 LYS cc_start: 0.8009 (ptmt) cc_final: 0.7590 (ptpp) REVERT: F 117 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.6735 (ttp80) REVERT: R 57 MET cc_start: 0.8216 (mmm) cc_final: 0.7990 (mmm) REVERT: R 78 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7068 (t80) REVERT: S 43 LYS cc_start: 0.8304 (mppt) cc_final: 0.8017 (mmmm) REVERT: S 208 GLU cc_start: 0.8083 (mp0) cc_final: 0.7637 (mp0) outliers start: 57 outliers final: 45 residues processed: 226 average time/residue: 0.0879 time to fit residues: 28.2750 Evaluate side-chains 230 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.171198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117963 restraints weight = 14247.534| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.10 r_work: 0.3488 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10396 Z= 0.113 Angle : 0.580 10.501 14098 Z= 0.299 Chirality : 0.042 0.169 1614 Planarity : 0.004 0.041 1783 Dihedral : 4.307 43.029 1448 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.20 % Allowed : 34.55 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.24), residues: 1323 helix: 0.80 (0.28), residues: 367 sheet: -0.17 (0.27), residues: 376 loop : -1.00 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 62 TYR 0.022 0.001 TYR E 373 PHE 0.023 0.001 PHE R 173 TRP 0.037 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00261 (10391) covalent geometry : angle 0.57743 (14088) SS BOND : bond 0.00356 ( 5) SS BOND : angle 2.23739 ( 10) hydrogen bonds : bond 0.02780 ( 456) hydrogen bonds : angle 4.47861 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: A 302 TYR cc_start: 0.8628 (t80) cc_final: 0.8291 (t80) REVERT: A 314 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7926 (mtpt) REVERT: B 130 GLU cc_start: 0.8956 (mp0) cc_final: 0.8708 (mp0) REVERT: B 234 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 338 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8297 (mp) REVERT: F 42 LYS cc_start: 0.8025 (ptmt) cc_final: 0.7601 (ptpp) REVERT: F 117 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.6783 (ttp80) REVERT: R 57 MET cc_start: 0.8159 (mmm) cc_final: 0.7925 (mmm) REVERT: S 43 LYS cc_start: 0.8263 (mppt) cc_final: 0.7986 (mmmm) REVERT: S 208 GLU cc_start: 0.8076 (mp0) cc_final: 0.7009 (mp0) REVERT: S 219 GLN cc_start: 0.7750 (pp30) cc_final: 0.7542 (pp30) outliers start: 45 outliers final: 40 residues processed: 214 average time/residue: 0.0932 time to fit residues: 28.2078 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 331 ASN C 11 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107549 restraints weight = 14440.174| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.09 r_work: 0.3308 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10396 Z= 0.277 Angle : 0.678 10.685 14098 Z= 0.358 Chirality : 0.046 0.183 1614 Planarity : 0.004 0.041 1783 Dihedral : 4.829 43.960 1448 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.05 % Rotamer: Outliers : 4.95 % Allowed : 33.61 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.23), residues: 1323 helix: 0.59 (0.28), residues: 366 sheet: -0.64 (0.26), residues: 372 loop : -1.15 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 168 TYR 0.029 0.002 TYR S 223 PHE 0.024 0.002 PHE R 140 TRP 0.039 0.002 TRP B 297 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00648 (10391) covalent geometry : angle 0.67540 (14088) SS BOND : bond 0.00292 ( 5) SS BOND : angle 2.12351 ( 10) hydrogen bonds : bond 0.03375 ( 456) hydrogen bonds : angle 4.82592 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.16 seconds wall clock time: 47 minutes 42.90 seconds (2862.90 seconds total)