Starting phenix.real_space_refine on Sun Dec 29 07:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_34993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_34993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_34993.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_34993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsc_34993/12_2024/8hsc_34993.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} 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: 5.98, per 1000 atoms: 0.59 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.14 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: 3.23 Time building geometry restraints manager: 2.98 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- 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 10391 Z= 0.232 Angle : 0.696 10.276 14088 Z= 0.365 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 : 7.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (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 TRP 0.027 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.034 0.002 PHE R 173 TYR 0.024 0.002 TYR A 302 ARG 0.012 0.000 ARG S 168 *********************** 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 : 1.168 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: 0.2324 time to fit residues: 56.9409 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 : 1.125 ------------------------------------------------------------------------------- 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 110 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN C 11 GLN R 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10391 Z= 0.347 Angle : 0.606 6.936 14088 Z= 0.326 Chirality : 0.044 0.177 1614 Planarity : 0.004 0.057 1783 Dihedral : 5.013 59.295 1451 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.88 % Allowed : 31.56 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1323 helix: 0.10 (0.28), residues: 371 sheet: -0.49 (0.26), residues: 384 loop : -1.09 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE B 241 TYR 0.023 0.002 TYR S 223 ARG 0.003 0.000 ARG S 168 *********************** 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 243 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: A 184 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8919 (tt) REVERT: A 302 TYR cc_start: 0.8627 (t80) cc_final: 0.8347 (t80) REVERT: B 59 TYR cc_start: 0.9120 (m-80) cc_final: 0.8751 (m-80) REVERT: F 58 GLN cc_start: 0.6828 (tm-30) cc_final: 0.6624 (tm-30) REVERT: F 117 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.6787 (ttp80) REVERT: R 78 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6964 (t80) REVERT: R 134 MET cc_start: 0.7528 (mpp) cc_final: 0.7283 (mpp) REVERT: R 175 TRP cc_start: 0.7063 (m100) cc_final: 0.6840 (m100) REVERT: S 72 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6448 (ptm-80) REVERT: S 219 GLN cc_start: 0.7794 (pp30) cc_final: 0.7507 (pp30) outliers start: 63 outliers final: 32 residues processed: 224 average time/residue: 0.2359 time to fit residues: 73.1330 Evaluate side-chains 208 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 VAL Chi-restraints excluded: chain B residue 133 VAL 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 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 122 CYS Chi-restraints excluded: chain R residue 128 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 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10391 Z= 0.326 Angle : 0.588 6.906 14088 Z= 0.314 Chirality : 0.043 0.168 1614 Planarity : 0.004 0.052 1783 Dihedral : 4.818 43.352 1449 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.72 % Allowed : 31.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1323 helix: 0.40 (0.28), residues: 374 sheet: -0.48 (0.26), residues: 377 loop : -1.12 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 267 HIS 0.005 0.001 HIS B 91 PHE 0.013 0.002 PHE R 35 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG B 197 *********************** 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 245 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 302 TYR cc_start: 0.8673 (t80) cc_final: 0.8430 (t80) REVERT: A 306 GLN cc_start: 0.8000 (tt0) cc_final: 0.7618 (tt0) REVERT: B 59 TYR cc_start: 0.9087 (m-80) cc_final: 0.8872 (m-80) REVERT: B 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: C 58 GLU cc_start: 0.8531 (pm20) cc_final: 0.8213 (pm20) REVERT: F 56 ILE cc_start: 0.8979 (mp) cc_final: 0.8771 (tp) REVERT: F 117 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.6672 (ttp80) REVERT: R 78 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6989 (t80) REVERT: R 147 ASP cc_start: 0.8666 (t0) cc_final: 0.8463 (t0) REVERT: R 175 TRP cc_start: 0.7166 (m100) cc_final: 0.6932 (m100) REVERT: S 72 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6452 (ptm-80) REVERT: S 219 GLN cc_start: 0.7776 (pp30) cc_final: 0.7248 (pp30) outliers start: 72 outliers final: 42 residues processed: 222 average time/residue: 0.2254 time to fit residues: 70.2026 Evaluate side-chains 215 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 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 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 77 THR Chi-restraints excluded: chain F residue 99 PHE 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 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 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 281 VAL 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 116 THR 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 117 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 R 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10391 Z= 0.257 Angle : 0.552 7.119 14088 Z= 0.294 Chirality : 0.042 0.168 1614 Planarity : 0.004 0.050 1783 Dihedral : 4.657 40.922 1449 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.98 % Allowed : 32.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1323 helix: 0.63 (0.29), residues: 372 sheet: -0.49 (0.26), residues: 386 loop : -1.10 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 267 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE R 173 TYR 0.020 0.001 TYR S 223 ARG 0.004 0.000 ARG B 197 *********************** 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 240 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 287 TYR cc_start: 0.8183 (m-80) cc_final: 0.7939 (m-80) REVERT: A 298 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: A 302 TYR cc_start: 0.8662 (t80) cc_final: 0.8383 (t80) REVERT: A 306 GLN cc_start: 0.7975 (tt0) cc_final: 0.7681 (tt0) REVERT: B 130 GLU cc_start: 0.8862 (mp0) cc_final: 0.8526 (mp0) REVERT: B 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: F 42 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7522 (ptpp) REVERT: F 56 ILE cc_start: 0.8991 (mp) cc_final: 0.8756 (tp) REVERT: F 117 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.6631 (ttp80) REVERT: R 78 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.7011 (t80) REVERT: R 147 ASP cc_start: 0.8687 (t0) cc_final: 0.8442 (t0) REVERT: R 175 TRP cc_start: 0.7176 (m100) cc_final: 0.6963 (m100) REVERT: S 219 GLN cc_start: 0.7785 (pp30) cc_final: 0.7524 (pp30) outliers start: 64 outliers final: 43 residues processed: 224 average time/residue: 0.2136 time to fit residues: 67.8479 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 14 GLU 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 316 THR Chi-restraints excluded: chain B residue 51 LEU 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 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 62 GLN Chi-restraints excluded: chain F residue 99 PHE 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 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 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 281 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 83 MET Chi-restraints excluded: chain S residue 116 THR 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 105 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 183 HIS C 11 GLN ** R 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 10391 Z= 0.590 Angle : 0.722 8.213 14088 Z= 0.388 Chirality : 0.049 0.195 1614 Planarity : 0.005 0.048 1783 Dihedral : 5.247 39.922 1448 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 9.24 % Allowed : 29.79 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1323 helix: 0.25 (0.28), residues: 373 sheet: -0.99 (0.25), residues: 378 loop : -1.32 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 297 HIS 0.008 0.002 HIS B 91 PHE 0.022 0.002 PHE B 241 TYR 0.037 0.002 TYR S 223 ARG 0.004 0.001 ARG R 236 *********************** 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 279 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 180 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6279 (mm110) cc_final: 0.5334 (mm110) REVERT: A 14 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: A 298 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: A 305 CYS cc_start: 0.8305 (m) cc_final: 0.8103 (t) REVERT: A 306 GLN cc_start: 0.8168 (tt0) cc_final: 0.7733 (tt0) REVERT: A 314 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7816 (mtpt) REVERT: B 45 MET cc_start: 0.8753 (mtp) cc_final: 0.8420 (mtt) REVERT: B 59 TYR cc_start: 0.9191 (m-80) cc_final: 0.8964 (m-80) REVERT: B 234 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: F 42 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7519 (ptpp) REVERT: F 56 ILE cc_start: 0.8942 (mp) cc_final: 0.8664 (tp) REVERT: F 117 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.6629 (ttp80) REVERT: R 78 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7149 (t80) REVERT: S 43 LYS cc_start: 0.8528 (mppt) cc_final: 0.8244 (mmmm) REVERT: S 72 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6592 (ptm-80) outliers start: 99 outliers final: 74 residues processed: 252 average time/residue: 0.2263 time to fit residues: 80.8244 Evaluate side-chains 253 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 173 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 32 ARG 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 269 ASN 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 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 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 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 F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 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 F residue 130 ASP Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 34 LEU 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 119 CYS 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 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 246 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 278 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 21 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN C 11 GLN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10391 Z= 0.155 Angle : 0.552 7.381 14088 Z= 0.288 Chirality : 0.041 0.167 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.524 39.463 1448 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.14 % Allowed : 33.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1323 helix: 0.70 (0.28), residues: 373 sheet: -0.38 (0.26), residues: 365 loop : -1.17 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 267 HIS 0.006 0.001 HIS S 35 PHE 0.019 0.001 PHE R 173 TYR 0.020 0.001 TYR A 302 ARG 0.004 0.000 ARG S 190 *********************** 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 244 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6446 (mm110) cc_final: 0.5497 (mm110) REVERT: A 269 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: A 287 TYR cc_start: 0.8045 (m-80) cc_final: 0.7844 (m-80) REVERT: A 298 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 314 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: B 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: B 297 TRP cc_start: 0.8507 (m100) cc_final: 0.8039 (m100) REVERT: C 47 GLU cc_start: 0.8388 (pm20) cc_final: 0.8057 (pm20) REVERT: F 42 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7602 (ptpp) REVERT: F 56 ILE cc_start: 0.8957 (mp) cc_final: 0.8673 (tp) REVERT: F 114 TYR cc_start: 0.7219 (m-80) cc_final: 0.6671 (m-80) REVERT: F 117 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.6755 (ttp80) REVERT: R 78 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.7090 (t80) REVERT: R 147 ASP cc_start: 0.8666 (t0) cc_final: 0.8418 (t0) REVERT: S 43 LYS cc_start: 0.8379 (mppt) cc_final: 0.8098 (mmmm) REVERT: S 208 GLU cc_start: 0.7880 (mp0) cc_final: 0.7173 (mp0) REVERT: S 210 GLU cc_start: 0.7522 (pm20) cc_final: 0.7220 (pm20) REVERT: S 219 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7364 (pp30) outliers start: 55 outliers final: 31 residues processed: 231 average time/residue: 0.2164 time to fit residues: 70.7930 Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 101 MET 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 336 LEU 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 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS 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 102 VAL 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 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 219 GLN 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 122 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10391 Z= 0.219 Angle : 0.583 13.010 14088 Z= 0.304 Chirality : 0.042 0.226 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.513 40.854 1448 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.58 % Allowed : 34.08 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1323 helix: 0.82 (0.29), residues: 366 sheet: -0.35 (0.26), residues: 367 loop : -1.21 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 64 TYR 0.020 0.001 TYR S 223 ARG 0.003 0.000 ARG R 117 *********************** 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 234 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: E 375 GLN cc_start: 0.5963 (mm110) cc_final: 0.5177 (mm-40) REVERT: A 298 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: A 306 GLN cc_start: 0.7901 (tt0) cc_final: 0.7676 (tt0) REVERT: A 314 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7812 (mtpt) REVERT: B 234 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: B 297 TRP cc_start: 0.8718 (m100) cc_final: 0.8494 (m100) REVERT: B 318 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8503 (mp) REVERT: F 42 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7558 (ptpp) REVERT: F 56 ILE cc_start: 0.8956 (mp) cc_final: 0.8661 (tp) REVERT: F 114 TYR cc_start: 0.7165 (m-80) cc_final: 0.6525 (m-80) REVERT: F 117 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6596 (ttp80) REVERT: R 78 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.7104 (t80) REVERT: R 147 ASP cc_start: 0.8644 (t0) cc_final: 0.8440 (t0) REVERT: S 43 LYS cc_start: 0.8353 (mppt) cc_final: 0.8086 (mmmm) REVERT: S 72 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6174 (ptm-80) REVERT: S 113 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8292 (tp-100) REVERT: S 208 GLU cc_start: 0.7901 (mp0) cc_final: 0.7142 (mp0) outliers start: 49 outliers final: 36 residues processed: 223 average time/residue: 0.2275 time to fit residues: 71.1406 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET 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 318 LEU 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 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 56 LEU 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 105 SER 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 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 72 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 177 ILE 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 78 optimal weight: 7.9990 chunk 50 optimal weight: 0.0770 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10391 Z= 0.364 Angle : 0.615 8.630 14088 Z= 0.328 Chirality : 0.045 0.228 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.752 41.368 1448 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.76 % Allowed : 33.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1323 helix: 0.61 (0.28), residues: 372 sheet: -0.56 (0.26), residues: 374 loop : -1.20 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 297 HIS 0.005 0.001 HIS B 142 PHE 0.034 0.002 PHE R 140 TYR 0.025 0.002 TYR S 223 ARG 0.004 0.000 ARG C 62 *********************** 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 234 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: A 314 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7856 (mtpt) REVERT: B 234 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 318 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 47 GLU cc_start: 0.8521 (pm20) cc_final: 0.8224 (pm20) REVERT: F 42 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7562 (ptpp) REVERT: F 114 TYR cc_start: 0.7154 (m-80) cc_final: 0.6607 (m-80) REVERT: F 117 ARG cc_start: 0.7457 (ttp-170) cc_final: 0.6568 (ttp80) REVERT: R 147 ASP cc_start: 0.8672 (t0) cc_final: 0.8415 (t0) REVERT: S 43 LYS cc_start: 0.8389 (mppt) cc_final: 0.8097 (mmmm) REVERT: S 72 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6310 (ptm-80) REVERT: S 113 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8334 (tp-100) outliers start: 51 outliers final: 43 residues processed: 223 average time/residue: 0.2245 time to fit residues: 70.1517 Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 269 ASN 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 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 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 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 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 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 SER 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 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 72 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10391 Z= 0.186 Angle : 0.572 9.421 14088 Z= 0.298 Chirality : 0.042 0.223 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.503 40.884 1448 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.20 % Allowed : 34.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1323 helix: 0.77 (0.29), residues: 366 sheet: -0.36 (0.26), residues: 375 loop : -1.16 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.001 PHE R 140 TYR 0.023 0.001 TYR E 373 ARG 0.002 0.000 ARG B 197 *********************** 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 236 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: A 306 GLN cc_start: 0.7815 (tt0) cc_final: 0.7603 (tt0) REVERT: A 314 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7791 (mtpt) REVERT: B 130 GLU cc_start: 0.8833 (mp0) cc_final: 0.8489 (mp0) REVERT: B 234 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: B 297 TRP cc_start: 0.8578 (m100) cc_final: 0.8199 (m100) REVERT: B 318 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8483 (mp) REVERT: F 42 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7563 (ptpp) REVERT: F 56 ILE cc_start: 0.8879 (mp) cc_final: 0.8570 (tp) REVERT: F 114 TYR cc_start: 0.7138 (m-80) cc_final: 0.6419 (m-80) REVERT: F 117 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6583 (ttp80) REVERT: R 147 ASP cc_start: 0.8619 (t0) cc_final: 0.8386 (t0) REVERT: S 43 LYS cc_start: 0.8374 (mppt) cc_final: 0.8088 (mmmm) REVERT: S 72 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6134 (ptm-80) REVERT: S 113 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8294 (tp-100) REVERT: S 208 GLU cc_start: 0.7741 (mp0) cc_final: 0.7367 (mp0) REVERT: S 219 GLN cc_start: 0.7720 (pp30) cc_final: 0.7469 (pp30) outliers start: 45 outliers final: 36 residues processed: 225 average time/residue: 0.2229 time to fit residues: 70.3937 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS 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 318 LEU Chi-restraints excluded: chain B residue 336 LEU 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 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 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 281 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 150 SER 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 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.0170 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10391 Z= 0.209 Angle : 0.573 9.463 14088 Z= 0.300 Chirality : 0.042 0.207 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.492 41.470 1448 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.01 % Allowed : 34.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1323 helix: 0.77 (0.28), residues: 367 sheet: -0.40 (0.26), residues: 382 loop : -1.12 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE R 173 TYR 0.026 0.001 TYR E 373 ARG 0.002 0.000 ARG B 197 ********************** 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: 43 poor density : 185 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: A 306 GLN cc_start: 0.7773 (tt0) cc_final: 0.7484 (tt0) REVERT: A 314 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: B 130 GLU cc_start: 0.8853 (mp0) cc_final: 0.8506 (mp0) REVERT: B 234 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: B 297 TRP cc_start: 0.8670 (m100) cc_final: 0.8361 (m100) REVERT: B 318 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8428 (mp) REVERT: C 47 GLU cc_start: 0.8447 (pm20) cc_final: 0.7944 (tm-30) REVERT: F 42 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7583 (ptpp) REVERT: F 56 ILE cc_start: 0.8885 (mp) cc_final: 0.8528 (tp) REVERT: F 114 TYR cc_start: 0.7133 (m-80) cc_final: 0.6402 (m-80) REVERT: F 117 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6557 (ttp80) REVERT: R 147 ASP cc_start: 0.8668 (t0) cc_final: 0.8461 (t0) REVERT: S 43 LYS cc_start: 0.8366 (mppt) cc_final: 0.8086 (mmmm) REVERT: S 72 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6111 (ptm-80) REVERT: S 113 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8300 (tp-100) REVERT: S 219 GLN cc_start: 0.7702 (pp30) cc_final: 0.7418 (pp30) outliers start: 43 outliers final: 38 residues processed: 217 average time/residue: 0.2303 time to fit residues: 70.3671 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL 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 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 318 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 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 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 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 281 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 150 SER 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 31 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.165148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111560 restraints weight = 14264.196| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.09 r_work: 0.3361 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10391 Z= 0.243 Angle : 0.584 9.481 14088 Z= 0.307 Chirality : 0.043 0.211 1614 Planarity : 0.004 0.047 1783 Dihedral : 4.521 41.654 1448 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.30 % Allowed : 34.83 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1323 helix: 0.72 (0.28), residues: 367 sheet: -0.43 (0.26), residues: 374 loop : -1.16 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 267 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE R 78 TYR 0.019 0.001 TYR S 223 ARG 0.002 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.97 seconds wall clock time: 48 minutes 19.66 seconds (2899.66 seconds total)