Starting phenix.real_space_refine on Fri Feb 14 11:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_34993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_34993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_34993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_34993.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_34993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsc_34993/02_2025/8hsc_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-5592/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: 6.85, per 1000 atoms: 0.67 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 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: 1.39 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: 4.32 Time building geometry restraints manager: 3.16 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: 3.460 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: 0.290 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- 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 : 1.181 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: 0.2521 time to fit residues: 61.3898 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 : 1.193 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109634 restraints weight = 14293.042| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.10 r_work: 0.3334 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 1.128 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: A 184 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8867 (tt) REVERT: A 302 TYR cc_start: 0.8625 (t80) cc_final: 0.8369 (t80) REVERT: B 59 TYR cc_start: 0.9030 (m-80) cc_final: 0.8676 (m-80) REVERT: F 117 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.6796 (ttp80) REVERT: R 78 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6903 (t80) REVERT: R 134 MET cc_start: 0.7566 (mpp) cc_final: 0.7332 (mpp) REVERT: R 175 TRP cc_start: 0.7037 (m100) cc_final: 0.6792 (m100) REVERT: S 72 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6367 (ptm-80) REVERT: S 219 GLN cc_start: 0.7804 (pp30) cc_final: 0.7510 (pp30) outliers start: 63 outliers final: 32 residues processed: 224 average time/residue: 0.2441 time to fit residues: 75.7979 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 : 1.240 ------------------------------------------------------------------------------- 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 73 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 86 optimal weight: 0.0170 chunk 2 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN R 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117570 restraints weight = 14176.011| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.98 r_work: 0.3473 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10391 Z= 0.161 Angle : 0.525 6.630 14088 Z= 0.279 Chirality : 0.041 0.162 1614 Planarity : 0.004 0.053 1783 Dihedral : 4.484 45.045 1449 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.01 % Allowed : 33.89 % Favored : 62.09 % 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: -0.65 (0.24), residues: 1323 helix: 0.54 (0.28), residues: 373 sheet: -0.32 (0.26), residues: 380 loop : -1.07 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 267 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE R 78 TYR 0.016 0.001 TYR S 178 ARG 0.006 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 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8270 (m-80) cc_final: 0.7692 (m-80) REVERT: A 302 TYR cc_start: 0.8642 (t80) cc_final: 0.8393 (t80) REVERT: A 306 GLN cc_start: 0.7982 (tt0) cc_final: 0.7735 (tt0) REVERT: B 130 GLU cc_start: 0.8873 (mp0) cc_final: 0.8667 (mp0) REVERT: B 234 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: F 117 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.6796 (ttp80) outliers start: 43 outliers final: 28 residues processed: 211 average time/residue: 0.2368 time to fit residues: 70.7758 Evaluate side-chains 202 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.157599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103353 restraints weight = 14582.843| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.08 r_work: 0.3240 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 10391 Z= 0.716 Angle : 0.789 12.605 14088 Z= 0.423 Chirality : 0.051 0.224 1614 Planarity : 0.005 0.047 1783 Dihedral : 5.334 41.205 1448 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 8.87 % Allowed : 29.69 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.28), residues: 372 sheet: -0.97 (0.25), residues: 395 loop : -1.29 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 297 HIS 0.008 0.002 HIS B 91 PHE 0.024 0.003 PHE B 241 TYR 0.038 0.002 TYR S 223 ARG 0.005 0.001 ARG R 117 *********************** 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 274 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 179 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6459 (mm110) cc_final: 0.5468 (mm-40) REVERT: A 14 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: A 298 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: A 306 GLN cc_start: 0.8374 (tt0) cc_final: 0.8094 (tt0) REVERT: B 234 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: B 318 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8629 (mp) REVERT: F 42 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7531 (ptpp) REVERT: F 56 ILE cc_start: 0.9018 (mp) cc_final: 0.8769 (tp) REVERT: F 117 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6655 (ttp80) REVERT: R 57 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8171 (tpt) REVERT: R 78 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7133 (t80) REVERT: S 43 LYS cc_start: 0.8547 (mppt) cc_final: 0.8280 (mmmm) REVERT: S 72 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7069 (ptm-80) REVERT: S 113 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8365 (tp-100) outliers start: 95 outliers final: 65 residues processed: 244 average time/residue: 0.2146 time to fit residues: 74.5938 Evaluate side-chains 248 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 348 PHE 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 269 ASN Chi-restraints excluded: chain A residue 298 GLU 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 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 232 ILE 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 292 PHE 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 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 70 ILE 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 34 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 57 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 98 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 252 VAL 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 113 GLN Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.165318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111747 restraints weight = 14190.498| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.07 r_work: 0.3366 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1741 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= 0.176 Angle : 0.548 7.282 14088 Z= 0.290 Chirality : 0.042 0.160 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.614 39.370 1448 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.04 % Allowed : 33.33 % 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 (0.23), residues: 1323 helix: 0.74 (0.29), residues: 370 sheet: -0.47 (0.27), residues: 353 loop : -1.17 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 267 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.001 PHE R 78 TYR 0.017 0.001 TYR A 302 ARG 0.004 0.000 ARG B 197 *********************** 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 238 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8159 (m-80) cc_final: 0.7907 (m-80) REVERT: A 298 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: A 314 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7847 (mtpt) REVERT: B 45 MET cc_start: 0.8582 (mtp) cc_final: 0.8087 (mtt) REVERT: B 234 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: F 42 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7536 (ptpp) REVERT: F 56 ILE cc_start: 0.9006 (mp) cc_final: 0.8742 (tp) REVERT: F 114 TYR cc_start: 0.7219 (m-80) cc_final: 0.6843 (m-80) REVERT: F 117 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6700 (ttp80) REVERT: R 78 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6917 (t80) REVERT: R 270 MET cc_start: 0.7405 (ptt) cc_final: 0.7113 (ptt) REVERT: S 43 LYS cc_start: 0.8398 (mppt) cc_final: 0.8099 (mmmm) REVERT: S 72 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6583 (ptm-80) REVERT: S 190 ARG cc_start: 0.7074 (ptt-90) cc_final: 0.6780 (ptt-90) REVERT: S 208 GLU cc_start: 0.7846 (mp0) cc_final: 0.7310 (mp0) REVERT: S 219 GLN cc_start: 0.7755 (pp30) cc_final: 0.7378 (pp30) outliers start: 54 outliers final: 36 residues processed: 221 average time/residue: 0.2300 time to fit residues: 70.9973 Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 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 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 64 LEU 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 132 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 281 VAL 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 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109101 restraints weight = 14474.053| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.11 r_work: 0.3331 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10391 Z= 0.288 Angle : 0.581 6.937 14088 Z= 0.309 Chirality : 0.043 0.164 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.647 40.926 1448 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.88 % Allowed : 33.05 % Favored : 61.06 % 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: -0.75 (0.24), residues: 1323 helix: 0.68 (0.29), residues: 373 sheet: -0.56 (0.26), residues: 374 loop : -1.16 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 267 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE R 173 TYR 0.021 0.001 TYR S 223 ARG 0.003 0.000 ARG C 62 *********************** 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 245 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8197 (m-80) cc_final: 0.7897 (m-80) REVERT: A 298 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: A 302 TYR cc_start: 0.8675 (t80) cc_final: 0.8290 (t80) REVERT: A 306 GLN cc_start: 0.8131 (tt0) cc_final: 0.7880 (tt0) REVERT: A 314 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7877 (mtpt) REVERT: B 45 MET cc_start: 0.8686 (mtp) cc_final: 0.8191 (mtt) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: C 47 GLU cc_start: 0.8565 (pm20) cc_final: 0.8289 (pm20) REVERT: F 42 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7576 (ptpp) REVERT: F 56 ILE cc_start: 0.8994 (mp) cc_final: 0.8675 (tp) REVERT: F 114 TYR cc_start: 0.7250 (m-80) cc_final: 0.6848 (m-80) REVERT: F 117 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.6621 (ttp80) REVERT: R 78 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.7034 (t80) REVERT: S 43 LYS cc_start: 0.8433 (mppt) cc_final: 0.8126 (mmmm) REVERT: S 72 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6317 (ptm-80) REVERT: S 113 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8312 (tp-100) REVERT: S 219 GLN cc_start: 0.7729 (pp30) cc_final: 0.7378 (pp30) outliers start: 63 outliers final: 48 residues processed: 228 average time/residue: 0.2265 time to fit residues: 72.1769 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 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 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 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 50 LEU 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 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 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 245 THR 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 72 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.161445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107351 restraints weight = 14568.292| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.11 r_work: 0.3302 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10391 Z= 0.406 Angle : 0.634 8.034 14088 Z= 0.338 Chirality : 0.045 0.177 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.854 40.788 1448 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.44 % Allowed : 32.31 % 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: -0.92 (0.24), residues: 1323 helix: 0.59 (0.28), residues: 373 sheet: -0.79 (0.25), residues: 386 loop : -1.19 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 267 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.002 PHE B 241 TYR 0.027 0.002 TYR S 223 ARG 0.004 0.000 ARG C 62 *********************** 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 254 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: A 302 TYR cc_start: 0.8698 (t80) cc_final: 0.8444 (t80) REVERT: A 314 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7859 (mtpt) REVERT: B 45 MET cc_start: 0.8748 (mtp) cc_final: 0.8367 (mtt) REVERT: B 130 GLU cc_start: 0.8947 (mp0) cc_final: 0.8614 (mp0) REVERT: B 234 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: B 318 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 47 GLU cc_start: 0.8696 (pm20) cc_final: 0.8394 (pm20) REVERT: F 42 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7575 (ptpp) REVERT: F 56 ILE cc_start: 0.8973 (mp) cc_final: 0.8644 (tp) REVERT: F 114 TYR cc_start: 0.7242 (m-80) cc_final: 0.6831 (m-80) REVERT: F 117 ARG cc_start: 0.7403 (ttp-170) cc_final: 0.6551 (ttp80) REVERT: R 78 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.7108 (t80) REVERT: S 43 LYS cc_start: 0.8467 (mppt) cc_final: 0.8159 (mmmm) REVERT: S 72 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6404 (ptm-80) REVERT: S 113 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8331 (tp-100) outliers start: 69 outliers final: 53 residues processed: 234 average time/residue: 0.2200 time to fit residues: 72.8499 Evaluate side-chains 243 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 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 51 LEU 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 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 300 LEU 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 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 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 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 245 THR Chi-restraints excluded: chain R residue 246 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 83 MET Chi-restraints excluded: chain S residue 113 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 293 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112327 restraints weight = 14290.402| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.09 r_work: 0.3375 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1899 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= 0.181 Angle : 0.561 8.697 14088 Z= 0.295 Chirality : 0.042 0.190 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.509 40.358 1448 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.76 % Allowed : 33.80 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.29), residues: 367 sheet: -0.45 (0.26), residues: 377 loop : -1.11 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.001 PHE R 173 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG E 310 *********************** 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 241 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8076 (m-80) cc_final: 0.7661 (m-80) REVERT: A 298 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 302 TYR cc_start: 0.8681 (t80) cc_final: 0.8403 (t80) REVERT: A 314 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7838 (mtpt) REVERT: B 45 MET cc_start: 0.8738 (mtp) cc_final: 0.8469 (mtt) REVERT: B 234 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: B 297 TRP cc_start: 0.8407 (m100) cc_final: 0.8072 (m100) REVERT: B 325 MET cc_start: 0.8491 (tpp) cc_final: 0.8277 (tpp) REVERT: C 47 GLU cc_start: 0.8563 (pm20) cc_final: 0.8271 (pm20) REVERT: F 42 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7560 (ptpp) REVERT: F 56 ILE cc_start: 0.8979 (mp) cc_final: 0.8636 (tp) REVERT: F 114 TYR cc_start: 0.7283 (m-80) cc_final: 0.6986 (m-80) REVERT: F 117 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.6612 (ttp80) REVERT: R 78 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7115 (t80) REVERT: S 43 LYS cc_start: 0.8398 (mppt) cc_final: 0.8096 (mmmm) REVERT: S 72 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6435 (ptm-80) outliers start: 51 outliers final: 37 residues processed: 230 average time/residue: 0.2189 time to fit residues: 70.7279 Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS 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 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 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 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 85 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 R 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.161553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107453 restraints weight = 14488.978| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.09 r_work: 0.3310 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10391 Z= 0.391 Angle : 0.637 9.273 14088 Z= 0.340 Chirality : 0.045 0.198 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.823 41.100 1448 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.51 % Allowed : 32.87 % 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: -0.84 (0.23), residues: 1323 helix: 0.62 (0.28), residues: 373 sheet: -0.66 (0.27), residues: 359 loop : -1.19 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 297 HIS 0.007 0.001 HIS B 142 PHE 0.053 0.002 PHE R 140 TYR 0.027 0.002 TYR S 223 ARG 0.003 0.000 ARG C 62 *********************** 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 244 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: E 375 GLN cc_start: 0.5561 (mm110) cc_final: 0.5119 (mt0) REVERT: A 287 TYR cc_start: 0.8259 (m-80) cc_final: 0.7726 (m-80) REVERT: A 298 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: A 302 TYR cc_start: 0.8681 (t80) cc_final: 0.8308 (t80) REVERT: A 314 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7836 (mtpt) REVERT: B 45 MET cc_start: 0.8751 (mtp) cc_final: 0.8528 (mtt) REVERT: B 130 GLU cc_start: 0.8960 (mp0) cc_final: 0.8594 (mp0) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: C 47 GLU cc_start: 0.8685 (pm20) cc_final: 0.8396 (pm20) REVERT: F 42 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7597 (ptpp) REVERT: F 114 TYR cc_start: 0.7261 (m-80) cc_final: 0.6726 (m-80) REVERT: F 117 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.6566 (ttp80) REVERT: R 78 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.7139 (t80) REVERT: S 43 LYS cc_start: 0.8452 (mppt) cc_final: 0.8129 (mmmm) REVERT: S 72 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6411 (ptm-80) REVERT: S 208 GLU cc_start: 0.8010 (mp0) cc_final: 0.7566 (mp0) outliers start: 59 outliers final: 46 residues processed: 229 average time/residue: 0.2271 time to fit residues: 73.4013 Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP 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 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 270 ILE 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 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 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 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 281 VAL 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 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 4 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 C 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.166849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113377 restraints weight = 14288.259| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.09 r_work: 0.3384 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10391 Z= 0.180 Angle : 0.581 9.456 14088 Z= 0.304 Chirality : 0.043 0.282 1614 Planarity : 0.004 0.047 1783 Dihedral : 4.521 40.455 1448 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.20 % Allowed : 33.99 % Favored : 61.81 % 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: -0.57 (0.24), residues: 1323 helix: 0.77 (0.29), residues: 367 sheet: -0.38 (0.27), residues: 372 loop : -1.05 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.047 0.001 PHE R 140 TYR 0.018 0.001 TYR E 373 ARG 0.003 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 233 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: A 314 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: B 45 MET cc_start: 0.8731 (mtp) cc_final: 0.8507 (mtt) REVERT: B 130 GLU cc_start: 0.8928 (mp0) cc_final: 0.8648 (mp0) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: B 325 MET cc_start: 0.8427 (tpp) cc_final: 0.8207 (tpp) REVERT: C 47 GLU cc_start: 0.8584 (pm20) cc_final: 0.8290 (pm20) REVERT: F 42 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7551 (ptpp) REVERT: F 114 TYR cc_start: 0.7212 (m-80) cc_final: 0.6521 (m-80) REVERT: F 117 ARG cc_start: 0.7408 (ttp-170) cc_final: 0.6579 (ttp80) REVERT: R 57 MET cc_start: 0.8022 (mmm) cc_final: 0.7815 (mmm) REVERT: R 78 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6969 (t80) REVERT: S 43 LYS cc_start: 0.8376 (mppt) cc_final: 0.8077 (mmmm) REVERT: S 72 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6377 (ptm-80) REVERT: S 208 GLU cc_start: 0.7909 (mp0) cc_final: 0.7478 (mp0) outliers start: 45 outliers final: 37 residues processed: 221 average time/residue: 0.2208 time to fit residues: 68.8433 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 : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain 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 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU 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 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 281 VAL 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 116 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 77 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109514 restraints weight = 14416.447| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.10 r_work: 0.3337 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10391 Z= 0.332 Angle : 0.618 9.450 14088 Z= 0.329 Chirality : 0.045 0.226 1614 Planarity : 0.004 0.045 1783 Dihedral : 4.688 41.312 1448 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 4.20 % Allowed : 34.36 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.24), residues: 1323 helix: 0.70 (0.29), residues: 366 sheet: -0.44 (0.27), residues: 347 loop : -1.20 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 267 HIS 0.006 0.001 HIS B 142 PHE 0.066 0.002 PHE R 140 TYR 0.023 0.002 TYR S 223 ARG 0.002 0.000 ARG B 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5957.91 seconds wall clock time: 106 minutes 30.97 seconds (6390.97 seconds total)