Starting phenix.real_space_refine on Mon Jul 6 21:10:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9b_27962/07_2026/8e9b_27962.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 C 24757 2.51 5 N 6659 2.21 5 O 7483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39160 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3156 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Chain: "B" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3089 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain: "C" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2825 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2584 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 301} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1390 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 161} Chain: "F" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1377 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1183 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "M" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.63, per 1000 atoms: 0.22 Number of scatterers: 39160 At special positions: 0 Unit cell: (222.332, 218.24, 129.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 O 7483 8.00 N 6659 7.00 C 24757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 257 " distance=2.82 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9202 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 76 sheets defined 48.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.870A pdb=" N MET A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 135 through 149 removed outlier: 3.579A pdb=" N ARG A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 4.173A pdb=" N TRP A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.519A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.358A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.807A pdb=" N THR A 337 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.596A pdb=" N GLN A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.748A pdb=" N TYR A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 403' Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.919A pdb=" N MET B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.692A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.870A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 4.013A pdb=" N VAL B 175 " --> pdb=" O ASN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.051A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.973A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.208A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.512A pdb=" N SER B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 325 removed outlier: 3.534A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 348 through 361 removed outlier: 3.786A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'C' and resid 316 through 330 Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 58 through 65 Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 120 through 140 removed outlier: 3.502A pdb=" N ASP D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 155 removed outlier: 4.086A pdb=" N LEU D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 206 removed outlier: 4.039A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 removed outlier: 3.692A pdb=" N GLN D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.526A pdb=" N ILE D 226 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG D 227 " --> pdb=" O LEU D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 227' Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.906A pdb=" N THR D 251 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 296 removed outlier: 5.398A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 removed outlier: 4.291A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 123 through 150 removed outlier: 3.527A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.549A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.598A pdb=" N ILE F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.774A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 101 Processing helix chain 'F' and resid 119 through 126 removed outlier: 3.900A pdb=" N THR F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 167 removed outlier: 4.523A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 167 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 removed outlier: 3.956A pdb=" N GLU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 49 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 51 through 61 Processing helix chain 'G' and resid 69 through 86 Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.514A pdb=" N PHE G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 116 Processing helix chain 'G' and resid 122 through 137 removed outlier: 3.980A pdb=" N LEU G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'M' and resid 55 through 62 Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 97 through 101 removed outlier: 3.644A pdb=" N GLU M 100 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS M 101 " --> pdb=" O PRO M 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 97 through 101' Processing helix chain 'M' and resid 112 through 128 removed outlier: 3.539A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE M 127 " --> pdb=" O MET M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 172 through 175 Processing helix chain 'M' and resid 181 through 194 removed outlier: 3.815A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.568A pdb=" N CYS M 217 " --> pdb=" O LYS M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 232 removed outlier: 4.097A pdb=" N SER M 232 " --> pdb=" O ALA M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 257 removed outlier: 3.860A pdb=" N CYS M 257 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 285 Processing helix chain 'M' and resid 289 through 296 removed outlier: 3.668A pdb=" N LEU M 293 " --> pdb=" O ILE M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 3.947A pdb=" N TYR M 306 " --> pdb=" O THR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 removed outlier: 3.957A pdb=" N ARG M 312 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 349 Processing helix chain 'M' and resid 350 through 353 Processing helix chain 'M' and resid 358 through 366 removed outlier: 4.387A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 removed outlier: 4.139A pdb=" N ARG M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 62 Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'N' and resid 97 through 101 removed outlier: 3.509A pdb=" N HIS N 101 " --> pdb=" O PRO N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.863A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 146 Processing helix chain 'N' and resid 172 through 175 removed outlier: 3.556A pdb=" N ILE N 175 " --> pdb=" O PRO N 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 172 through 175' Processing helix chain 'N' and resid 181 through 197 removed outlier: 4.055A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY N 197 " --> pdb=" O LEU N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 217 Processing helix chain 'N' and resid 222 through 232 removed outlier: 3.639A pdb=" N SER N 232 " --> pdb=" O ALA N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.521A pdb=" N ARG N 256 " --> pdb=" O ASN N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 284 removed outlier: 3.699A pdb=" N THR N 278 " --> pdb=" O ILE N 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR N 279 " --> pdb=" O HIS N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 296 Processing helix chain 'N' and resid 302 through 306 removed outlier: 3.500A pdb=" N MET N 305 " --> pdb=" O GLY N 302 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR N 306 " --> pdb=" O THR N 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 302 through 306' Processing helix chain 'N' and resid 308 through 321 removed outlier: 3.751A pdb=" N ARG N 312 " --> pdb=" O GLY N 308 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET N 313 " --> pdb=" O ILE N 309 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN N 314 " --> pdb=" O ALA N 310 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR N 318 " --> pdb=" O GLN N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 348 Processing helix chain 'N' and resid 359 through 366 removed outlier: 4.434A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 374 removed outlier: 3.814A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 97 through 101 removed outlier: 3.637A pdb=" N HIS O 101 " --> pdb=" O PRO O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.765A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 181 through 195 removed outlier: 3.584A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 216 removed outlier: 3.741A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 230 Processing helix chain 'O' and resid 252 through 260 removed outlier: 3.733A pdb=" N CYS O 257 " --> pdb=" O GLU O 253 " (cutoff:3.500A) Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 261 through 262 No H-bonds generated for 'chain 'O' and resid 261 through 262' Processing helix chain 'O' and resid 263 through 268 Processing helix chain 'O' and resid 273 through 285 removed outlier: 3.757A pdb=" N TYR O 279 " --> pdb=" O HIS O 275 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 295 removed outlier: 3.604A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 306 removed outlier: 3.703A pdb=" N TYR O 306 " --> pdb=" O THR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 removed outlier: 3.940A pdb=" N ARG O 312 " --> pdb=" O GLY O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 336 No H-bonds generated for 'chain 'O' and resid 334 through 336' Processing helix chain 'O' and resid 337 through 348 removed outlier: 3.509A pdb=" N SER O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 356 removed outlier: 3.674A pdb=" N GLN O 353 " --> pdb=" O SER O 350 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN O 354 " --> pdb=" O THR O 351 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP O 356 " --> pdb=" O GLN O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 366 Processing helix chain 'O' and resid 368 through 374 Processing helix chain 'P' and resid 55 through 62 Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 78 through 92 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.727A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 Processing helix chain 'P' and resid 172 through 175 removed outlier: 4.164A pdb=" N ILE P 175 " --> pdb=" O PRO P 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 172 through 175' Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.812A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY P 197 " --> pdb=" O LEU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 216 removed outlier: 3.521A pdb=" N LYS P 215 " --> pdb=" O ASP P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 230 Processing helix chain 'P' and resid 252 through 257 removed outlier: 3.846A pdb=" N CYS P 257 " --> pdb=" O GLU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 262 Processing helix chain 'P' and resid 263 through 268 removed outlier: 3.545A pdb=" N ILE P 267 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 284 Processing helix chain 'P' and resid 289 through 296 removed outlier: 3.681A pdb=" N LEU P 293 " --> pdb=" O ILE P 289 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 306 removed outlier: 3.793A pdb=" N TYR P 306 " --> pdb=" O THR P 303 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 334 through 336 No H-bonds generated for 'chain 'P' and resid 334 through 336' Processing helix chain 'P' and resid 337 through 348 Processing helix chain 'P' and resid 351 through 356 removed outlier: 3.907A pdb=" N GLN P 354 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 366 removed outlier: 3.807A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 374 removed outlier: 3.866A pdb=" N ARG P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 78 through 92 Processing helix chain 'Q' and resid 97 through 101 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.745A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 146 Processing helix chain 'Q' and resid 172 through 175 removed outlier: 3.652A pdb=" N ILE Q 175 " --> pdb=" O PRO Q 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 172 through 175' Processing helix chain 'Q' and resid 181 through 193 Processing helix chain 'Q' and resid 194 through 197 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 222 through 232 removed outlier: 3.749A pdb=" N SER Q 232 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.857A pdb=" N CYS Q 257 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 261 Processing helix chain 'Q' and resid 263 through 268 Processing helix chain 'Q' and resid 275 through 284 Processing helix chain 'Q' and resid 286 through 294 removed outlier: 3.550A pdb=" N ARG Q 290 " --> pdb=" O ASP Q 286 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 306 removed outlier: 3.802A pdb=" N TYR Q 306 " --> pdb=" O THR Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 334 through 336 No H-bonds generated for 'chain 'Q' and resid 334 through 336' Processing helix chain 'Q' and resid 337 through 348 Processing helix chain 'Q' and resid 349 through 356 removed outlier: 4.327A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP Q 356 " --> pdb=" O GLN Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 368 through 374 removed outlier: 3.742A pdb=" N ARG Q 372 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 78 through 92 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.714A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 171 through 175 Processing helix chain 'R' and resid 181 through 194 removed outlier: 3.770A pdb=" N THR R 194 " --> pdb=" O MET R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 202 through 216 Processing helix chain 'R' and resid 222 through 232 removed outlier: 3.800A pdb=" N SER R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 257 removed outlier: 3.976A pdb=" N CYS R 257 " --> pdb=" O GLU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 261 Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 273 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing helix chain 'R' and resid 289 through 296 Processing helix chain 'R' and resid 302 through 306 removed outlier: 3.866A pdb=" N TYR R 306 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 Processing helix chain 'R' and resid 334 through 336 No H-bonds generated for 'chain 'R' and resid 334 through 336' Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 351 through 356 removed outlier: 3.730A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP R 356 " --> pdb=" O GLN R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 364 removed outlier: 3.779A pdb=" N GLU R 364 " --> pdb=" O GLN R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 367 No H-bonds generated for 'chain 'R' and resid 365 through 367' Processing helix chain 'R' and resid 368 through 374 removed outlier: 4.091A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS R 373 " --> pdb=" O ILE R 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.542A pdb=" N GLN H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 93 Processing helix chain 'H' and resid 112 through 128 removed outlier: 4.147A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.905A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.665A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 216 Processing helix chain 'H' and resid 222 through 230 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.721A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.717A pdb=" N CYS H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 294 removed outlier: 4.151A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.516A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.575A pdb=" N ARG H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 356 removed outlier: 3.979A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 355 " --> pdb=" O PHE H 352 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP H 356 " --> pdb=" O GLN H 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 356' Processing helix chain 'H' and resid 359 through 366 removed outlier: 4.359A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 374 removed outlier: 3.752A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.512A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.669A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 145 removed outlier: 3.939A pdb=" N SER I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 3.705A pdb=" N ILE I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 194 Processing helix chain 'I' and resid 202 through 216 removed outlier: 3.584A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 230 Processing helix chain 'I' and resid 252 through 260 removed outlier: 3.628A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 261 through 262 No H-bonds generated for 'chain 'I' and resid 261 through 262' Processing helix chain 'I' and resid 263 through 268 removed outlier: 3.789A pdb=" N PHE I 266 " --> pdb=" O GLN I 263 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY I 268 " --> pdb=" O SER I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.727A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 306 removed outlier: 3.953A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 removed outlier: 3.535A pdb=" N ARG I 312 " --> pdb=" O GLY I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 351 through 355 removed outlier: 3.945A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 363 removed outlier: 4.215A pdb=" N TYR I 362 " --> pdb=" O THR I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.852A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.113A pdb=" N TYR A 29 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.782A pdb=" N LYS A 207 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.329A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.624A pdb=" N PHE B 27 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 103 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 160 through 165 removed outlier: 6.933A pdb=" N ILE B 297 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.565A pdb=" N TYR B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 9 removed outlier: 6.881A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 367 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA C 362 " --> pdb=" O PRO C 352 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 364 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 350 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 366 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.286A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 37 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 64 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 64 removed outlier: 3.559A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.982A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 128 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 137 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.900A pdb=" N CYS C 165 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 210 through 213 removed outlier: 3.998A pdb=" N ALA C 210 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 254 through 261 removed outlier: 6.304A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP C 289 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 276 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 278 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 285 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.566A pdb=" N PHE D 88 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER D 89 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS D 80 " --> pdb=" O SER D 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 157 through 162 removed outlier: 4.305A pdb=" N TYR D 161 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 245 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 214 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 56 removed outlier: 3.615A pdb=" N ARG F 55 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 8 through 11 removed outlier: 3.598A pdb=" N PHE M 31 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA M 29 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'M' and resid 105 through 107 removed outlier: 6.681A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'M' and resid 176 through 178 Processing sheet with id=AD4, first strand: chain 'M' and resid 165 through 166 Processing sheet with id=AD5, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.537A pdb=" N PHE N 31 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.542A pdb=" N VAL N 35 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'N' and resid 176 through 178 removed outlier: 6.409A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 165 through 166 Processing sheet with id=AE2, first strand: chain 'N' and resid 238 through 241 removed outlier: 3.881A pdb=" N ILE N 250 " --> pdb=" O LYS N 238 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 17 through 21 removed outlier: 4.263A pdb=" N THR O 106 " --> pdb=" O CYS O 10 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASN O 12 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.540A pdb=" N TYR O 53 " --> pdb=" O GLY O 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL O 35 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG O 37 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AE6, first strand: chain 'O' and resid 176 through 178 removed outlier: 3.540A pdb=" N VAL O 152 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 238 through 241 removed outlier: 3.895A pdb=" N LYS O 238 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE O 250 " --> pdb=" O LYS O 238 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 8 through 11 Processing sheet with id=AE9, first strand: chain 'P' and resid 35 through 36 Processing sheet with id=AF1, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AF2, first strand: chain 'P' and resid 105 through 107 removed outlier: 6.918A pdb=" N LEU P 105 " --> pdb=" O ALA P 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'P' and resid 131 through 132 removed outlier: 3.697A pdb=" N MET P 132 " --> pdb=" O ILE P 357 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE P 357 " --> pdb=" O MET P 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'P' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'P' and resid 169 through 170 removed outlier: 6.776A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN P 297 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AF7, first strand: chain 'Q' and resid 8 through 12 removed outlier: 3.628A pdb=" N PHE Q 31 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AF9, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AG1, first strand: chain 'Q' and resid 103 through 106 Processing sheet with id=AG2, first strand: chain 'Q' and resid 176 through 178 removed outlier: 3.704A pdb=" N VAL Q 152 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN Q 297 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 165 through 166 Processing sheet with id=AG4, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AG5, first strand: chain 'R' and resid 8 through 10 removed outlier: 4.140A pdb=" N THR R 106 " --> pdb=" O CYS R 10 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 16 through 19 removed outlier: 3.527A pdb=" N ALA R 29 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.537A pdb=" N VAL R 35 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AG9, first strand: chain 'R' and resid 176 through 178 removed outlier: 3.500A pdb=" N HIS R 161 " --> pdb=" O ASP R 154 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP R 154 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL R 163 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL R 152 " --> pdb=" O VAL R 163 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 238 through 241 removed outlier: 3.523A pdb=" N LYS R 238 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 8 through 12 removed outlier: 3.594A pdb=" N LYS H 18 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.986A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS H 68 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AH5, first strand: chain 'H' and resid 105 through 107 removed outlier: 6.476A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'H' and resid 131 through 132 removed outlier: 3.531A pdb=" N MET H 132 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 176 through 178 removed outlier: 3.663A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AH9, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE I 31 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN I 12 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AI2, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AI3, first strand: chain 'I' and resid 176 through 178 removed outlier: 3.513A pdb=" N MET I 176 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 300 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER I 155 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 238 through 241 1749 hydrogen bonds defined for protein. 4749 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: 9.26 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 12245 1.33 - 1.45: 5879 1.45 - 1.57: 21477 1.57 - 1.69: 32 1.69 - 1.81: 395 Bond restraints: 40028 Sorted by residual: bond pdb=" C4 ATP B 902 " pdb=" C5 ATP B 902 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.33e+01 bond pdb=" C5 ATP B 902 " pdb=" C6 ATP B 902 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C8 ATP B 902 " pdb=" N7 ATP B 902 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C4 ATP B 902 " pdb=" N9 ATP B 902 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.90e+01 ... (remaining 40023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 54041 3.83 - 7.66: 271 7.66 - 11.48: 12 11.48 - 15.31: 0 15.31 - 19.14: 2 Bond angle restraints: 54326 Sorted by residual: angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 120.73 19.14 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PA ATP B 902 " pdb=" O3A ATP B 902 " pdb=" PB ATP B 902 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP B 902 " pdb=" C4 ATP B 902 " pdb=" N3 ATP B 902 " ideal model delta sigma weight residual 126.80 118.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" N3 ATP B 902 " pdb=" C4 ATP B 902 " pdb=" N9 ATP B 902 " ideal model delta sigma weight residual 127.04 134.92 -7.88 1.15e+00 7.59e-01 4.72e+01 angle pdb=" N GLU N 253 " pdb=" CA GLU N 253 " pdb=" C GLU N 253 " ideal model delta sigma weight residual 112.38 119.99 -7.61 1.22e+00 6.72e-01 3.89e+01 ... (remaining 54321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 23417 33.36 - 66.73: 583 66.73 - 100.09: 56 100.09 - 133.45: 4 133.45 - 166.82: 8 Dihedral angle restraints: 24068 sinusoidal: 9747 harmonic: 14321 Sorted by residual: dihedral pdb=" CD ARG D 205 " pdb=" NE ARG D 205 " pdb=" CZ ARG D 205 " pdb=" NH1 ARG D 205 " ideal model delta sinusoidal sigma weight residual 0.00 -86.73 86.73 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CD ARG D 204 " pdb=" NE ARG D 204 " pdb=" CZ ARG D 204 " pdb=" NH1 ARG D 204 " ideal model delta sinusoidal sigma weight residual 0.00 67.42 -67.42 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CD ARG N 256 " pdb=" NE ARG N 256 " pdb=" CZ ARG N 256 " pdb=" NH1 ARG N 256 " ideal model delta sinusoidal sigma weight residual 0.00 -63.68 63.68 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 24065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5111 0.065 - 0.130: 870 0.130 - 0.195: 31 0.195 - 0.260: 3 0.260 - 0.325: 1 Chirality restraints: 6016 Sorted by residual: chirality pdb=" CA PHE N 255 " pdb=" N PHE N 255 " pdb=" C PHE N 255 " pdb=" CB PHE N 255 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU N 253 " pdb=" N GLU N 253 " pdb=" C GLU N 253 " pdb=" CB GLU N 253 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ARG D 162 " pdb=" N ARG D 162 " pdb=" C ARG D 162 " pdb=" CB ARG D 162 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 6013 not shown) Planarity restraints: 6988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 205 " 1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG D 205 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 205 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 205 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 205 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 204 " 1.017 9.50e-02 1.11e+02 4.56e-01 1.25e+02 pdb=" NE ARG D 204 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG D 204 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 204 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 204 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 256 " 0.987 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG N 256 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG N 256 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG N 256 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 256 " 0.024 2.00e-02 2.50e+03 ... (remaining 6985 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 389 2.60 - 3.17: 34348 3.17 - 3.75: 60998 3.75 - 4.32: 83038 4.32 - 4.90: 139321 Nonbonded interactions: 318094 Sorted by model distance: nonbonded pdb="MG MG R 801 " pdb=" O3B ADP R 802 " model vdw 2.023 2.170 nonbonded pdb="MG MG M 801 " pdb=" O3B ADP M 802 " model vdw 2.025 2.170 nonbonded pdb="MG MG Q 801 " pdb=" O3B ADP Q 802 " model vdw 2.048 2.170 nonbonded pdb="MG MG P 801 " pdb=" O3B ADP P 802 " model vdw 2.070 2.170 nonbonded pdb="MG MG N 801 " pdb=" O3B ADP N 802 " model vdw 2.086 2.170 ... (remaining 318089 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 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 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: 0.070 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 35.570 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.005 0.790 40029 Z= 0.281 Angle : 0.723 25.082 54328 Z= 0.400 Chirality : 0.046 0.325 6016 Planarity : 0.011 0.492 6988 Dihedral : 15.363 166.817 14863 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 0.24 % Allowed : 0.43 % Favored : 99.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4875 helix: 0.98 (0.12), residues: 1833 sheet: -0.62 (0.17), residues: 960 loop : -0.34 (0.15), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 147 TYR 0.034 0.001 TYR H 166 PHE 0.030 0.001 PHE M 352 TRP 0.095 0.003 TRP Q 340 HIS 0.010 0.001 HIS H 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 (40028) covalent geometry : angle 0.70740 / 0.39 (54326) SS BOND : bond 0.78963 / 41.56 ( 1) SS BOND : angle 24.93740 / 16.62 ( 2) hydrogen bonds : bond 0.18236 / 12.87 ( 1733) hydrogen bonds : angle 6.72096 / 4.71 ( 4749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1266 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5108 (m-80) cc_final: 0.4437 (m-80) REVERT: A 18 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7330 (mptt) REVERT: A 140 GLU cc_start: 0.8335 (tt0) cc_final: 0.7880 (pt0) REVERT: A 151 ASN cc_start: 0.6197 (t0) cc_final: 0.5756 (t0) REVERT: A 214 ARG cc_start: 0.6847 (ttt90) cc_final: 0.6583 (ttm170) REVERT: A 267 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6825 (mtpp) REVERT: A 284 PHE cc_start: 0.6987 (p90) cc_final: 0.6475 (p90) REVERT: A 295 ASN cc_start: 0.8120 (t0) cc_final: 0.7310 (t0) REVERT: A 368 LYS cc_start: 0.8067 (pptt) cc_final: 0.7085 (mmtm) REVERT: A 382 GLN cc_start: 0.8346 (mm110) cc_final: 0.7905 (mm-40) REVERT: B 19 TYR cc_start: 0.7808 (m-80) cc_final: 0.7232 (m-10) REVERT: B 23 ASN cc_start: 0.7370 (m-40) cc_final: 0.7026 (m-40) REVERT: B 59 GLU cc_start: 0.6978 (pp20) cc_final: 0.6332 (pt0) REVERT: B 64 LEU cc_start: 0.8076 (mp) cc_final: 0.7861 (mt) REVERT: B 81 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 83 ASN cc_start: 0.8136 (m110) cc_final: 0.6977 (m-40) REVERT: B 111 ASN cc_start: 0.7788 (m-40) cc_final: 0.7570 (m-40) REVERT: B 133 TYR cc_start: 0.8061 (t80) cc_final: 0.7226 (t80) REVERT: B 183 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7182 (ttp80) REVERT: B 211 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 271 GLN cc_start: 0.8781 (mt0) cc_final: 0.8404 (mt0) REVERT: B 283 GLN cc_start: 0.7705 (tp40) cc_final: 0.7417 (mm110) REVERT: B 320 LEU cc_start: 0.8164 (tp) cc_final: 0.7775 (tp) REVERT: B 329 ASP cc_start: 0.7855 (t0) cc_final: 0.7324 (m-30) REVERT: B 345 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7671 (ptp-110) REVERT: C 46 LYS cc_start: 0.7722 (pttp) cc_final: 0.7084 (ttpp) REVERT: C 69 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6423 (mtm-85) REVERT: C 75 GLN cc_start: 0.7527 (tt0) cc_final: 0.7194 (tt0) REVERT: C 91 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7813 (ttpt) REVERT: C 130 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7064 (mp0) REVERT: C 135 TRP cc_start: 0.7748 (m-10) cc_final: 0.7196 (m100) REVERT: C 155 HIS cc_start: 0.7830 (t-90) cc_final: 0.7204 (t-90) REVERT: C 160 LEU cc_start: 0.8497 (mt) cc_final: 0.8263 (mp) REVERT: C 165 CYS cc_start: 0.8073 (t) cc_final: 0.7800 (t) REVERT: C 248 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8496 (mttp) REVERT: C 282 SER cc_start: 0.8651 (t) cc_final: 0.8302 (m) REVERT: C 366 SER cc_start: 0.7729 (p) cc_final: 0.7422 (m) REVERT: D 8 ASN cc_start: 0.7897 (t0) cc_final: 0.7601 (t0) REVERT: D 86 TYR cc_start: 0.7952 (m-80) cc_final: 0.7365 (m-80) REVERT: D 109 MET cc_start: 0.8267 (tpp) cc_final: 0.7993 (tpp) REVERT: D 119 LEU cc_start: 0.7953 (tp) cc_final: 0.7691 (tp) REVERT: D 125 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6864 (tmm-80) REVERT: D 186 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6058 (tm-30) REVERT: D 254 ASN cc_start: 0.7393 (t0) cc_final: 0.7039 (t0) REVERT: E 93 GLU cc_start: 0.7587 (mp0) cc_final: 0.7136 (mp0) REVERT: E 97 ASN cc_start: 0.7704 (m-40) cc_final: 0.7197 (m-40) REVERT: E 98 SER cc_start: 0.8163 (t) cc_final: 0.7717 (p) REVERT: F 3 ASN cc_start: 0.7785 (t0) cc_final: 0.7561 (m-40) REVERT: F 79 VAL cc_start: 0.9039 (t) cc_final: 0.8548 (m) REVERT: F 107 LYS cc_start: 0.8269 (mmmm) cc_final: 0.8019 (mtmt) REVERT: F 137 GLU cc_start: 0.7517 (tp30) cc_final: 0.7070 (tp30) REVERT: F 149 MET cc_start: 0.7620 (mtm) cc_final: 0.7260 (mtm) REVERT: G 100 SER cc_start: 0.7374 (p) cc_final: 0.6685 (t) REVERT: G 119 GLN cc_start: 0.8677 (pp30) cc_final: 0.8006 (pp30) REVERT: G 135 GLU cc_start: 0.8437 (tt0) cc_final: 0.8054 (pt0) REVERT: G 151 ASP cc_start: 0.6446 (p0) cc_final: 0.5777 (p0) REVERT: M 122 ILE cc_start: 0.7950 (mt) cc_final: 0.7623 (mm) REVERT: M 123 MET cc_start: 0.8213 (tpt) cc_final: 0.7432 (ttm) REVERT: M 128 ASN cc_start: 0.8368 (t0) cc_final: 0.8005 (m-40) REVERT: M 263 GLN cc_start: 0.8285 (mt0) cc_final: 0.7884 (mt0) REVERT: N 44 MET cc_start: 0.5012 (tpt) cc_final: 0.4794 (mtp) REVERT: N 82 MET cc_start: 0.8497 (tpp) cc_final: 0.8283 (tpt) REVERT: N 113 LYS cc_start: 0.8419 (ptpt) cc_final: 0.8197 (ptmt) REVERT: N 257 CYS cc_start: 0.7165 (t) cc_final: 0.6809 (t) REVERT: N 296 ASN cc_start: 0.7225 (m110) cc_final: 0.6936 (m-40) REVERT: N 316 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7901 (mm-30) REVERT: O 59 GLN cc_start: 0.8649 (tp40) cc_final: 0.8318 (mm-40) REVERT: O 149 THR cc_start: 0.7997 (p) cc_final: 0.7562 (t) REVERT: O 154 ASP cc_start: 0.7754 (t0) cc_final: 0.7420 (t0) REVERT: O 157 ASP cc_start: 0.8458 (t70) cc_final: 0.8030 (t0) REVERT: O 176 MET cc_start: 0.8179 (mmm) cc_final: 0.7654 (mmm) REVERT: O 242 LEU cc_start: 0.8825 (tp) cc_final: 0.8399 (mt) REVERT: O 253 GLU cc_start: 0.8147 (mp0) cc_final: 0.7896 (mp0) REVERT: O 263 GLN cc_start: 0.8616 (mt0) cc_final: 0.8357 (mt0) REVERT: O 299 MET cc_start: 0.8125 (mmm) cc_final: 0.7898 (mmm) REVERT: P 47 MET cc_start: 0.7010 (pmm) cc_final: 0.6382 (pmm) REVERT: P 69 TYR cc_start: 0.8388 (m-80) cc_final: 0.8119 (m-80) REVERT: P 89 THR cc_start: 0.8640 (m) cc_final: 0.8333 (p) REVERT: P 117 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7732 (mt-10) REVERT: P 121 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8217 (tm-30) REVERT: P 180 LEU cc_start: 0.9078 (tp) cc_final: 0.8863 (tp) REVERT: P 227 MET cc_start: 0.8794 (mmm) cc_final: 0.8355 (mmt) REVERT: P 299 MET cc_start: 0.8295 (mmm) cc_final: 0.8031 (tpt) REVERT: Q 47 MET cc_start: 0.7061 (mmm) cc_final: 0.5817 (ptt) REVERT: Q 59 GLN cc_start: 0.8659 (tp40) cc_final: 0.8167 (tm-30) REVERT: Q 106 THR cc_start: 0.8944 (m) cc_final: 0.8696 (p) REVERT: Q 132 MET cc_start: 0.7748 (ppp) cc_final: 0.7501 (ppp) REVERT: Q 227 MET cc_start: 0.8529 (mmm) cc_final: 0.8270 (mmm) REVERT: Q 283 MET cc_start: 0.8298 (mmm) cc_final: 0.7988 (mmp) REVERT: R 113 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7420 (mttp) REVERT: R 132 MET cc_start: 0.7831 (ppp) cc_final: 0.7380 (ppp) REVERT: R 208 ILE cc_start: 0.8638 (mt) cc_final: 0.8393 (mm) REVERT: R 229 THR cc_start: 0.7518 (m) cc_final: 0.7316 (m) REVERT: R 288 ASP cc_start: 0.5927 (p0) cc_final: 0.5617 (t0) REVERT: R 337 TYR cc_start: 0.8811 (m-80) cc_final: 0.8531 (m-80) REVERT: H 92 ASN cc_start: 0.7450 (m110) cc_final: 0.7102 (m110) REVERT: H 121 GLN cc_start: 0.8348 (tm130) cc_final: 0.8101 (tm-30) REVERT: H 180 LEU cc_start: 0.8302 (mt) cc_final: 0.7895 (mt) REVERT: H 236 LEU cc_start: 0.7856 (pt) cc_final: 0.7555 (mt) REVERT: H 237 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6134 (tp30) REVERT: H 238 LYS cc_start: 0.7152 (mmmm) cc_final: 0.6893 (mptt) REVERT: H 249 THR cc_start: 0.7696 (m) cc_final: 0.7179 (p) REVERT: H 286 ASP cc_start: 0.6854 (p0) cc_final: 0.6631 (p0) REVERT: H 294 TYR cc_start: 0.6952 (m-80) cc_final: 0.6567 (m-10) REVERT: H 313 MET cc_start: 0.8454 (tpt) cc_final: 0.8004 (tpp) REVERT: H 329 ILE cc_start: 0.8294 (mm) cc_final: 0.7755 (mt) REVERT: H 352 PHE cc_start: 0.7790 (t80) cc_final: 0.7480 (t80) REVERT: H 355 MET cc_start: 0.7142 (pmm) cc_final: 0.6899 (pmm) REVERT: H 367 PRO cc_start: 0.8009 (Cg_endo) cc_final: 0.7201 (Cg_exo) REVERT: I 12 ASN cc_start: 0.7546 (p0) cc_final: 0.7285 (p0) REVERT: I 62 ARG cc_start: 0.8235 (ptt180) cc_final: 0.7988 (ptp90) REVERT: I 107 GLU cc_start: 0.7472 (pm20) cc_final: 0.7054 (pm20) REVERT: I 153 LEU cc_start: 0.7638 (tp) cc_final: 0.7212 (tt) REVERT: I 173 HIS cc_start: 0.6260 (m170) cc_final: 0.5869 (m170) REVERT: I 222 ASP cc_start: 0.6548 (p0) cc_final: 0.6170 (p0) REVERT: I 227 MET cc_start: 0.7810 (ttt) cc_final: 0.7111 (mtp) REVERT: I 236 LEU cc_start: 0.7323 (pp) cc_final: 0.7033 (mt) REVERT: I 237 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5917 (mt-10) REVERT: I 241 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7135 (tm-30) REVERT: I 263 GLN cc_start: 0.8593 (mt0) cc_final: 0.8094 (mt0) REVERT: I 280 ASN cc_start: 0.7437 (m-40) cc_final: 0.7106 (m-40) REVERT: I 296 ASN cc_start: 0.5598 (t0) cc_final: 0.5342 (t0) REVERT: I 325 MET cc_start: 0.6316 (ppp) cc_final: 0.5985 (ppp) REVERT: I 352 PHE cc_start: 0.6539 (t80) cc_final: 0.6295 (t80) outliers start: 10 outliers final: 2 residues processed: 1270 average time/residue: 0.2482 time to fit residues: 500.1993 Evaluate side-chains 726 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 724 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain R residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN A 221 GLN A 316 GLN B 319 GLN C 209 HIS C 359 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 296 ASN F 58 GLN M 92 ASN M 101 HIS M 296 ASN N 12 ASN N 162 ASN O 40 HIS O 49 GLN O 88 HIS O 161 HIS P 12 ASN Q 40 HIS Q 111 ASN R 12 ASN R 161 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 246 GLN H 297 ASN H 371 HIS I 78 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 162 ASN I 354 GLN I 371 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089650 restraints weight = 89086.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091773 restraints weight = 46490.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093188 restraints weight = 29735.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094095 restraints weight = 21917.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094594 restraints weight = 17914.442| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.160 40029 Z= 0.323 Angle : 0.822 15.330 54328 Z= 0.416 Chirality : 0.052 0.183 6016 Planarity : 0.006 0.159 6988 Dihedral : 9.072 174.343 5517 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.76 % Favored : 94.22 % Rotamer: Outliers : 2.44 % Allowed : 14.54 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4875 helix: 0.51 (0.12), residues: 1830 sheet: -0.86 (0.17), residues: 967 loop : -0.57 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG I 116 TYR 0.023 0.002 TYR D 65 PHE 0.030 0.003 PHE A 150 TRP 0.058 0.003 TRP Q 340 HIS 0.010 0.002 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.32 (40028) covalent geometry : angle 0.82162 / 0.42 (54326) SS BOND : bond 0.02406 / 1.27 ( 1) SS BOND : angle 2.14909 / 1.43 ( 2) hydrogen bonds : bond 0.05234 / 3.55 ( 1733) hydrogen bonds : angle 5.58854 / 3.95 ( 4749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 697 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5119 (m-80) cc_final: 0.4387 (m-80) REVERT: A 133 LEU cc_start: 0.7593 (mp) cc_final: 0.7197 (tp) REVERT: A 140 GLU cc_start: 0.8286 (tt0) cc_final: 0.8054 (pt0) REVERT: A 234 LEU cc_start: 0.8143 (tt) cc_final: 0.7926 (tp) REVERT: A 295 ASN cc_start: 0.8346 (t0) cc_final: 0.7938 (t0) REVERT: A 368 LYS cc_start: 0.7917 (pptt) cc_final: 0.6789 (mmtm) REVERT: A 382 GLN cc_start: 0.8424 (mm110) cc_final: 0.8142 (tp-100) REVERT: A 420 TYR cc_start: 0.5053 (t80) cc_final: 0.4655 (t80) REVERT: B 19 TYR cc_start: 0.7671 (m-80) cc_final: 0.7245 (m-10) REVERT: B 64 LEU cc_start: 0.8128 (mp) cc_final: 0.7927 (mt) REVERT: B 81 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 107 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: B 133 TYR cc_start: 0.8134 (t80) cc_final: 0.7108 (t80) REVERT: B 227 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: B 237 MET cc_start: 0.8114 (mmm) cc_final: 0.7831 (mmt) REVERT: B 283 GLN cc_start: 0.8040 (tp40) cc_final: 0.7620 (mm110) REVERT: B 305 MET cc_start: 0.8809 (mmm) cc_final: 0.8514 (mmt) REVERT: B 324 ARG cc_start: 0.6939 (tpp80) cc_final: 0.6565 (tpp80) REVERT: B 329 ASP cc_start: 0.7791 (t0) cc_final: 0.7560 (m-30) REVERT: C 83 GLU cc_start: 0.6342 (pm20) cc_final: 0.5727 (pm20) REVERT: D 109 MET cc_start: 0.8678 (tpp) cc_final: 0.8299 (tpp) REVERT: D 129 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7734 (mmtp) REVERT: D 148 ASP cc_start: 0.6084 (m-30) cc_final: 0.5706 (m-30) REVERT: D 155 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6928 (mm-30) REVERT: D 280 MET cc_start: 0.8833 (mmt) cc_final: 0.8393 (mmt) REVERT: E 79 GLU cc_start: 0.6003 (tp30) cc_final: 0.5336 (tp30) REVERT: E 83 ARG cc_start: 0.4842 (tpp80) cc_final: 0.4557 (tpp80) REVERT: E 97 ASN cc_start: 0.7860 (m-40) cc_final: 0.7405 (m-40) REVERT: E 98 SER cc_start: 0.7969 (t) cc_final: 0.7510 (p) REVERT: F 9 LEU cc_start: 0.8208 (mt) cc_final: 0.7975 (mt) REVERT: F 89 LYS cc_start: 0.8117 (tppp) cc_final: 0.7886 (ttpt) REVERT: F 137 GLU cc_start: 0.7536 (tp30) cc_final: 0.6903 (tp30) REVERT: G 27 GLU cc_start: 0.7768 (tt0) cc_final: 0.7480 (tt0) REVERT: G 82 ASP cc_start: 0.8116 (m-30) cc_final: 0.7808 (m-30) REVERT: G 97 LYS cc_start: 0.6254 (pptt) cc_final: 0.6008 (pttp) REVERT: G 119 GLN cc_start: 0.8166 (pp30) cc_final: 0.7789 (tm-30) REVERT: G 128 ASN cc_start: 0.6746 (t0) cc_final: 0.6517 (t0) REVERT: G 151 ASP cc_start: 0.6366 (p0) cc_final: 0.5879 (p0) REVERT: M 122 ILE cc_start: 0.8372 (mt) cc_final: 0.8153 (mm) REVERT: N 44 MET cc_start: 0.5146 (tpt) cc_final: 0.4602 (mtm) REVERT: N 176 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: O 132 MET cc_start: 0.7338 (ppp) cc_final: 0.7100 (ppp) REVERT: O 206 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7804 (ttp80) REVERT: O 283 MET cc_start: 0.9028 (mmm) cc_final: 0.8797 (mmm) REVERT: O 337 TYR cc_start: 0.8037 (m-80) cc_final: 0.7761 (m-80) REVERT: P 69 TYR cc_start: 0.8332 (m-80) cc_final: 0.8053 (m-80) REVERT: P 89 THR cc_start: 0.8424 (m) cc_final: 0.8168 (p) REVERT: P 121 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8307 (tm-30) REVERT: Q 47 MET cc_start: 0.6890 (mmm) cc_final: 0.5874 (ptp) REVERT: Q 283 MET cc_start: 0.8427 (mmm) cc_final: 0.7958 (mmp) REVERT: R 137 GLN cc_start: 0.8029 (mt0) cc_final: 0.7783 (mp10) REVERT: R 269 MET cc_start: 0.8193 (ttm) cc_final: 0.7677 (ttm) REVERT: R 288 ASP cc_start: 0.5662 (p0) cc_final: 0.5344 (p0) REVERT: H 123 MET cc_start: 0.7858 (ttm) cc_final: 0.7521 (ttm) REVERT: H 140 LEU cc_start: 0.8750 (mt) cc_final: 0.8479 (mp) REVERT: H 236 LEU cc_start: 0.7908 (pt) cc_final: 0.7404 (mt) REVERT: H 237 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6796 (tm-30) REVERT: H 238 LYS cc_start: 0.7357 (mmmm) cc_final: 0.6630 (mptt) REVERT: H 249 THR cc_start: 0.8094 (m) cc_final: 0.7695 (p) REVERT: H 299 MET cc_start: 0.6573 (mtp) cc_final: 0.6300 (mtp) REVERT: H 305 MET cc_start: 0.6166 (tpp) cc_final: 0.5813 (tpt) REVERT: H 311 ASP cc_start: 0.7467 (m-30) cc_final: 0.7125 (m-30) REVERT: H 325 MET cc_start: 0.7313 (mmt) cc_final: 0.6899 (tpp) REVERT: H 329 ILE cc_start: 0.8165 (mm) cc_final: 0.7719 (mt) REVERT: H 352 PHE cc_start: 0.7787 (t80) cc_final: 0.6879 (t80) REVERT: H 356 TRP cc_start: 0.7603 (m100) cc_final: 0.6772 (m100) REVERT: I 82 MET cc_start: 0.8237 (mmt) cc_final: 0.7876 (mmm) REVERT: I 132 MET cc_start: 0.7795 (ppp) cc_final: 0.7167 (pmm) REVERT: I 207 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7716 (mm-30) REVERT: I 241 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7027 (tm-30) REVERT: I 263 GLN cc_start: 0.8391 (mt0) cc_final: 0.8179 (tt0) REVERT: I 280 ASN cc_start: 0.7622 (m-40) cc_final: 0.7106 (m-40) REVERT: I 325 MET cc_start: 0.6684 (ppp) cc_final: 0.5900 (ppp) outliers start: 103 outliers final: 68 residues processed: 766 average time/residue: 0.2579 time to fit residues: 317.5319 Evaluate side-chains 651 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 580 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain O residue 10 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 238 LYS Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 354 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 435 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 417 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 378 optimal weight: 3.9990 chunk 470 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 476 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN M 12 ASN M 296 ASN N 161 HIS R 92 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 173 HIS H 246 GLN H 297 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.110990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091955 restraints weight = 87529.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094141 restraints weight = 45038.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095583 restraints weight = 28451.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096501 restraints weight = 20858.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097088 restraints weight = 16990.966| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40029 Z= 0.144 Angle : 0.646 13.782 54328 Z= 0.322 Chirality : 0.045 0.186 6016 Planarity : 0.005 0.051 6988 Dihedral : 8.672 170.080 5514 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.54 % Allowed : 17.11 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4875 helix: 0.81 (0.12), residues: 1833 sheet: -0.68 (0.17), residues: 931 loop : -0.49 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 167 TYR 0.025 0.001 TYR D 65 PHE 0.018 0.001 PHE D 127 TRP 0.030 0.002 TRP Q 340 HIS 0.007 0.001 HIS H 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (40028) covalent geometry : angle 0.64619 / 0.32 (54326) SS BOND : bond 0.00982 / 0.52 ( 1) SS BOND : angle 2.02983 / 1.35 ( 2) hydrogen bonds : bond 0.04151 / 2.84 ( 1733) hydrogen bonds : angle 5.19351 / 3.67 ( 4749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 649 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.3643 (m-80) REVERT: A 83 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7717 (ttmm) REVERT: A 95 ARG cc_start: 0.7444 (ptp-110) cc_final: 0.7244 (ptp-170) REVERT: A 133 LEU cc_start: 0.7344 (mp) cc_final: 0.6949 (tp) REVERT: A 214 ARG cc_start: 0.6969 (ttm170) cc_final: 0.6513 (mtt180) REVERT: A 281 ASP cc_start: 0.7990 (t0) cc_final: 0.7724 (t0) REVERT: A 295 ASN cc_start: 0.8296 (t0) cc_final: 0.7928 (t0) REVERT: A 368 LYS cc_start: 0.7810 (pptt) cc_final: 0.6708 (mmtm) REVERT: A 382 GLN cc_start: 0.8408 (mm110) cc_final: 0.8109 (tp-100) REVERT: A 420 TYR cc_start: 0.4812 (t80) cc_final: 0.4527 (t80) REVERT: B 19 TYR cc_start: 0.7611 (m-80) cc_final: 0.7213 (m-10) REVERT: B 39 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6963 (mtm180) REVERT: B 64 LEU cc_start: 0.8073 (mp) cc_final: 0.7854 (mt) REVERT: B 81 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 107 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: B 133 TYR cc_start: 0.8060 (t80) cc_final: 0.6989 (t80) REVERT: B 227 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: B 283 GLN cc_start: 0.7856 (tp40) cc_final: 0.7422 (mm110) REVERT: B 324 ARG cc_start: 0.6907 (tpp80) cc_final: 0.6638 (tpp80) REVERT: B 329 ASP cc_start: 0.7742 (t0) cc_final: 0.7495 (m-30) REVERT: C 69 ARG cc_start: 0.6459 (mtt90) cc_final: 0.6237 (mtt90) REVERT: D 64 ASN cc_start: 0.8139 (t0) cc_final: 0.7502 (m-40) REVERT: D 109 MET cc_start: 0.8693 (tpp) cc_final: 0.8399 (tpp) REVERT: D 113 MET cc_start: 0.8026 (tpp) cc_final: 0.7360 (mmt) REVERT: D 129 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7840 (mmtp) REVERT: D 205 ARG cc_start: 0.7286 (mtm180) cc_final: 0.7052 (mtm110) REVERT: D 280 MET cc_start: 0.8631 (mmt) cc_final: 0.7800 (mmp) REVERT: E 79 GLU cc_start: 0.6011 (tp30) cc_final: 0.5796 (tp30) REVERT: E 97 ASN cc_start: 0.7929 (m-40) cc_final: 0.7274 (m110) REVERT: E 98 SER cc_start: 0.8202 (t) cc_final: 0.7649 (p) REVERT: E 159 LYS cc_start: 0.6649 (pttm) cc_final: 0.6123 (ttpp) REVERT: F 137 GLU cc_start: 0.7426 (tp30) cc_final: 0.6933 (tp30) REVERT: G 27 GLU cc_start: 0.7756 (tt0) cc_final: 0.7488 (tt0) REVERT: G 82 ASP cc_start: 0.8190 (m-30) cc_final: 0.7944 (m-30) REVERT: M 122 ILE cc_start: 0.8273 (mt) cc_final: 0.8019 (mm) REVERT: M 123 MET cc_start: 0.7681 (tpp) cc_final: 0.7039 (ttm) REVERT: N 44 MET cc_start: 0.5297 (tpt) cc_final: 0.4679 (mtm) REVERT: N 176 MET cc_start: 0.8003 (mtp) cc_final: 0.7745 (mtp) REVERT: O 84 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8460 (ttmt) REVERT: O 206 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7783 (ttp80) REVERT: O 330 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (mt) REVERT: O 337 TYR cc_start: 0.7909 (m-80) cc_final: 0.7606 (m-80) REVERT: P 69 TYR cc_start: 0.8322 (m-80) cc_final: 0.8084 (m-80) REVERT: P 89 THR cc_start: 0.8267 (m) cc_final: 0.8049 (p) REVERT: P 227 MET cc_start: 0.8806 (mmm) cc_final: 0.8168 (mmt) REVERT: Q 47 MET cc_start: 0.6608 (mmm) cc_final: 0.5716 (ptp) REVERT: Q 283 MET cc_start: 0.8466 (mmm) cc_final: 0.8120 (mmt) REVERT: R 269 MET cc_start: 0.8016 (ttm) cc_final: 0.7493 (ttm) REVERT: H 92 ASN cc_start: 0.7413 (m110) cc_final: 0.6615 (m110) REVERT: H 123 MET cc_start: 0.7747 (ttm) cc_final: 0.7336 (ttm) REVERT: H 140 LEU cc_start: 0.8736 (mt) cc_final: 0.8494 (mp) REVERT: H 236 LEU cc_start: 0.7805 (pt) cc_final: 0.7358 (mt) REVERT: H 249 THR cc_start: 0.8065 (m) cc_final: 0.7593 (p) REVERT: H 294 TYR cc_start: 0.6861 (m-80) cc_final: 0.6478 (m-80) REVERT: H 313 MET cc_start: 0.8162 (tpt) cc_final: 0.7791 (tpp) REVERT: H 325 MET cc_start: 0.7363 (mmt) cc_final: 0.6862 (mpp) REVERT: H 329 ILE cc_start: 0.8215 (mm) cc_final: 0.7800 (mt) REVERT: H 352 PHE cc_start: 0.8033 (t80) cc_final: 0.7392 (t80) REVERT: H 355 MET cc_start: 0.6886 (pmm) cc_final: 0.6449 (pmm) REVERT: H 356 TRP cc_start: 0.7544 (m100) cc_final: 0.6585 (m100) REVERT: I 82 MET cc_start: 0.8331 (mmt) cc_final: 0.7925 (mmm) REVERT: I 207 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7520 (mm-30) REVERT: I 227 MET cc_start: 0.8029 (ttt) cc_final: 0.7644 (mtp) REVERT: I 241 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7097 (tm-30) REVERT: I 263 GLN cc_start: 0.8283 (mt0) cc_final: 0.7951 (tt0) REVERT: I 280 ASN cc_start: 0.7461 (m-40) cc_final: 0.7130 (m110) REVERT: I 325 MET cc_start: 0.6693 (ppp) cc_final: 0.5912 (ppp) outliers start: 107 outliers final: 59 residues processed: 718 average time/residue: 0.2486 time to fit residues: 288.8766 Evaluate side-chains 639 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 576 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 160 optimal weight: 0.0070 chunk 345 optimal weight: 2.9990 chunk 408 optimal weight: 0.8980 chunk 359 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 384 optimal weight: 6.9990 chunk 296 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 73 GLN D 296 ASN F 58 GLN M 92 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 59 GLN H 173 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092762 restraints weight = 86051.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095033 restraints weight = 43543.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096519 restraints weight = 27167.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097493 restraints weight = 19702.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098114 restraints weight = 15877.708| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40029 Z= 0.114 Angle : 0.614 12.761 54328 Z= 0.303 Chirality : 0.045 0.198 6016 Planarity : 0.004 0.045 6988 Dihedral : 8.266 171.020 5514 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.47 % Allowed : 17.70 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4875 helix: 0.98 (0.12), residues: 1839 sheet: -0.58 (0.17), residues: 943 loop : -0.36 (0.15), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 138 TYR 0.023 0.001 TYR A 246 PHE 0.023 0.001 PHE B 24 TRP 0.020 0.001 TRP M 340 HIS 0.005 0.001 HIS M 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (40028) covalent geometry : angle 0.61425 / 0.30 (54326) SS BOND : bond 0.01755 / 0.92 ( 1) SS BOND : angle 1.80777 / 1.21 ( 2) hydrogen bonds : bond 0.03642 / 2.49 ( 1733) hydrogen bonds : angle 4.96816 / 3.51 ( 4749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 634 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5145 (OUTLIER) cc_final: 0.3770 (m-80) REVERT: A 83 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7635 (ttmm) REVERT: A 133 LEU cc_start: 0.7294 (mp) cc_final: 0.6963 (tp) REVERT: A 214 ARG cc_start: 0.7003 (ttm170) cc_final: 0.6675 (ttm170) REVERT: A 231 ASP cc_start: 0.7397 (t0) cc_final: 0.7134 (t0) REVERT: A 281 ASP cc_start: 0.7999 (t0) cc_final: 0.7591 (t0) REVERT: A 295 ASN cc_start: 0.8358 (t0) cc_final: 0.7928 (t0) REVERT: A 368 LYS cc_start: 0.7758 (pptt) cc_final: 0.6659 (mmtm) REVERT: A 382 GLN cc_start: 0.8398 (mm110) cc_final: 0.8099 (tp-100) REVERT: B 19 TYR cc_start: 0.7593 (m-80) cc_final: 0.7072 (m-10) REVERT: B 39 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6944 (mtm180) REVERT: B 64 LEU cc_start: 0.7950 (mp) cc_final: 0.7715 (mt) REVERT: B 72 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: B 81 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 107 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: B 133 TYR cc_start: 0.7997 (t80) cc_final: 0.6890 (t80) REVERT: B 227 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: B 283 GLN cc_start: 0.7733 (tp40) cc_final: 0.7256 (mm110) REVERT: B 320 LEU cc_start: 0.8139 (tp) cc_final: 0.7903 (tp) REVERT: B 324 ARG cc_start: 0.7037 (tpp80) cc_final: 0.6808 (tpp80) REVERT: B 329 ASP cc_start: 0.7656 (t0) cc_final: 0.7264 (m-30) REVERT: C 69 ARG cc_start: 0.6506 (mtt90) cc_final: 0.6236 (mtt90) REVERT: C 91 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7794 (ttpp) REVERT: C 258 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6647 (tp) REVERT: D 109 MET cc_start: 0.8660 (tpp) cc_final: 0.8365 (tpp) REVERT: D 113 MET cc_start: 0.7999 (tpp) cc_final: 0.7317 (mmt) REVERT: D 118 VAL cc_start: 0.8094 (p) cc_final: 0.7823 (p) REVERT: D 129 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7795 (mmtp) REVERT: D 280 MET cc_start: 0.8746 (mmt) cc_final: 0.8408 (mmt) REVERT: E 79 GLU cc_start: 0.5995 (tp30) cc_final: 0.5593 (tp30) REVERT: E 83 ARG cc_start: 0.5529 (tpp80) cc_final: 0.5255 (tpp80) REVERT: E 97 ASN cc_start: 0.7886 (m-40) cc_final: 0.7455 (m-40) REVERT: E 98 SER cc_start: 0.8208 (t) cc_final: 0.7625 (p) REVERT: E 159 LYS cc_start: 0.6574 (pttm) cc_final: 0.5931 (ttpp) REVERT: F 58 GLN cc_start: 0.8306 (mp-120) cc_final: 0.8044 (mm-40) REVERT: G 22 PHE cc_start: 0.8465 (m-80) cc_final: 0.8259 (m-80) REVERT: G 27 GLU cc_start: 0.7783 (tt0) cc_final: 0.7474 (tt0) REVERT: G 82 ASP cc_start: 0.8242 (m-30) cc_final: 0.7998 (m-30) REVERT: G 151 ASP cc_start: 0.6866 (p0) cc_final: 0.6545 (p0) REVERT: M 122 ILE cc_start: 0.8069 (mt) cc_final: 0.7803 (mm) REVERT: M 123 MET cc_start: 0.7612 (tpp) cc_final: 0.7040 (ttm) REVERT: M 325 MET cc_start: 0.7087 (ptm) cc_final: 0.6855 (ptm) REVERT: N 44 MET cc_start: 0.5385 (tpt) cc_final: 0.4656 (mtm) REVERT: O 84 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8474 (ttmt) REVERT: O 206 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7811 (ttp80) REVERT: O 330 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8298 (mt) REVERT: O 337 TYR cc_start: 0.7930 (m-80) cc_final: 0.7576 (m-80) REVERT: P 47 MET cc_start: 0.6880 (pmm) cc_final: 0.6556 (pmm) REVERT: P 69 TYR cc_start: 0.8261 (m-80) cc_final: 0.8017 (m-80) REVERT: P 83 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7749 (mt-10) REVERT: P 227 MET cc_start: 0.8830 (mmm) cc_final: 0.8211 (mmt) REVERT: Q 47 MET cc_start: 0.6552 (mmm) cc_final: 0.5691 (ptp) REVERT: Q 283 MET cc_start: 0.8490 (mmm) cc_final: 0.8161 (mmt) REVERT: H 123 MET cc_start: 0.7688 (ttm) cc_final: 0.7173 (ttm) REVERT: H 140 LEU cc_start: 0.8719 (mt) cc_final: 0.8481 (mp) REVERT: H 236 LEU cc_start: 0.7743 (pt) cc_final: 0.7458 (mt) REVERT: H 249 THR cc_start: 0.8094 (m) cc_final: 0.7634 (p) REVERT: H 286 ASP cc_start: 0.7272 (p0) cc_final: 0.6311 (p0) REVERT: H 290 ARG cc_start: 0.7308 (mtm180) cc_final: 0.6687 (mtm180) REVERT: H 294 TYR cc_start: 0.7069 (m-80) cc_final: 0.6547 (m-80) REVERT: H 313 MET cc_start: 0.8141 (tpt) cc_final: 0.7801 (tpp) REVERT: H 325 MET cc_start: 0.7347 (mmt) cc_final: 0.6950 (tpp) REVERT: H 329 ILE cc_start: 0.8130 (mm) cc_final: 0.7921 (mt) REVERT: H 352 PHE cc_start: 0.7863 (t80) cc_final: 0.7463 (t80) REVERT: H 355 MET cc_start: 0.6807 (pmm) cc_final: 0.6237 (pmm) REVERT: H 356 TRP cc_start: 0.7368 (m100) cc_final: 0.6313 (m100) REVERT: I 82 MET cc_start: 0.8380 (mmt) cc_final: 0.7958 (mmm) REVERT: I 154 ASP cc_start: 0.8179 (t70) cc_final: 0.7365 (t70) REVERT: I 227 MET cc_start: 0.7953 (ttt) cc_final: 0.7607 (mtp) REVERT: I 241 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7293 (tm-30) REVERT: I 263 GLN cc_start: 0.8355 (mt0) cc_final: 0.7908 (tt0) REVERT: I 280 ASN cc_start: 0.7389 (m-40) cc_final: 0.7048 (m110) REVERT: I 314 GLN cc_start: 0.6601 (tp40) cc_final: 0.6266 (tp40) REVERT: I 316 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7337 (mm-30) REVERT: I 325 MET cc_start: 0.6628 (ppp) cc_final: 0.5786 (ppp) outliers start: 104 outliers final: 64 residues processed: 701 average time/residue: 0.2399 time to fit residues: 274.1401 Evaluate side-chains 651 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 580 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 338 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 481 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 59 GLN I 49 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087604 restraints weight = 88041.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089678 restraints weight = 45999.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091032 restraints weight = 29448.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091904 restraints weight = 21789.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092443 restraints weight = 17881.580| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 40029 Z= 0.361 Angle : 0.804 12.597 54328 Z= 0.404 Chirality : 0.052 0.195 6016 Planarity : 0.006 0.061 6988 Dihedral : 8.555 165.324 5514 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.89 % Allowed : 18.77 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4875 helix: 0.48 (0.12), residues: 1833 sheet: -0.84 (0.17), residues: 963 loop : -0.63 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 138 TYR 0.048 0.003 TYR G 112 PHE 0.024 0.002 PHE Q 127 TRP 0.030 0.003 TRP E 160 HIS 0.008 0.002 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.36 (40028) covalent geometry : angle 0.80342 / 0.40 (54326) SS BOND : bond 0.02087 / 1.10 ( 1) SS BOND : angle 2.75683 / 1.84 ( 2) hydrogen bonds : bond 0.05072 / 3.45 ( 1733) hydrogen bonds : angle 5.36639 / 3.79 ( 4749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 566 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4087 (m-80) REVERT: A 95 ARG cc_start: 0.7445 (ptp-170) cc_final: 0.7102 (ptp-170) REVERT: A 147 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (m-10) REVERT: A 231 ASP cc_start: 0.7367 (t0) cc_final: 0.7069 (t0) REVERT: B 19 TYR cc_start: 0.7655 (m-80) cc_final: 0.7114 (m-10) REVERT: B 64 LEU cc_start: 0.8094 (mp) cc_final: 0.7882 (mt) REVERT: B 77 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.5897 (mpt180) REVERT: B 107 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: B 133 TYR cc_start: 0.8177 (t80) cc_final: 0.7089 (t80) REVERT: B 227 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7390 (t-90) REVERT: B 277 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7491 (t80) REVERT: B 283 GLN cc_start: 0.8127 (tp40) cc_final: 0.7651 (mm110) REVERT: B 320 LEU cc_start: 0.8376 (tp) cc_final: 0.8009 (tp) REVERT: B 324 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6591 (tpp80) REVERT: B 361 MET cc_start: 0.7709 (ttp) cc_final: 0.7438 (ttp) REVERT: C 91 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7670 (ttpp) REVERT: C 131 GLN cc_start: 0.7067 (tm-30) cc_final: 0.6817 (tm-30) REVERT: C 286 HIS cc_start: 0.8075 (t70) cc_final: 0.7564 (t70) REVERT: D 109 MET cc_start: 0.8699 (tpp) cc_final: 0.8466 (tpp) REVERT: D 129 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7897 (mmtp) REVERT: D 205 ARG cc_start: 0.7355 (mtm180) cc_final: 0.7059 (mtm110) REVERT: E 97 ASN cc_start: 0.7725 (m-40) cc_final: 0.7330 (m-40) REVERT: E 98 SER cc_start: 0.8524 (t) cc_final: 0.7838 (p) REVERT: F 130 LYS cc_start: 0.7963 (ptpt) cc_final: 0.7748 (ttmm) REVERT: F 137 GLU cc_start: 0.7636 (tp30) cc_final: 0.7177 (tp30) REVERT: G 82 ASP cc_start: 0.8212 (m-30) cc_final: 0.7964 (m-30) REVERT: G 87 ILE cc_start: 0.7104 (mt) cc_final: 0.6844 (mt) REVERT: G 151 ASP cc_start: 0.6752 (p0) cc_final: 0.6356 (p0) REVERT: M 122 ILE cc_start: 0.8360 (mt) cc_final: 0.8124 (mm) REVERT: M 123 MET cc_start: 0.7917 (tpp) cc_final: 0.7317 (ttm) REVERT: N 44 MET cc_start: 0.5426 (tpt) cc_final: 0.4541 (mtm) REVERT: O 206 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7742 (ttp80) REVERT: O 337 TYR cc_start: 0.7945 (m-80) cc_final: 0.7659 (m-80) REVERT: P 64 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8809 (mp) REVERT: P 69 TYR cc_start: 0.8191 (m-80) cc_final: 0.7933 (m-80) REVERT: P 227 MET cc_start: 0.8800 (mmm) cc_final: 0.8543 (mmt) REVERT: P 287 ILE cc_start: 0.9098 (tp) cc_final: 0.8897 (tp) REVERT: Q 47 MET cc_start: 0.6650 (mmm) cc_final: 0.5801 (ptp) REVERT: Q 283 MET cc_start: 0.8490 (mmm) cc_final: 0.7964 (mmp) REVERT: R 269 MET cc_start: 0.8181 (ttm) cc_final: 0.7742 (ttm) REVERT: R 276 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7632 (mt-10) REVERT: H 140 LEU cc_start: 0.8837 (mt) cc_final: 0.8609 (mp) REVERT: H 236 LEU cc_start: 0.7771 (pt) cc_final: 0.7272 (mt) REVERT: H 249 THR cc_start: 0.8179 (m) cc_final: 0.7793 (p) REVERT: H 294 TYR cc_start: 0.7122 (m-80) cc_final: 0.6526 (m-10) REVERT: H 305 MET cc_start: 0.5972 (tpt) cc_final: 0.5747 (tpt) REVERT: H 313 MET cc_start: 0.8183 (tpt) cc_final: 0.7757 (tpp) REVERT: H 352 PHE cc_start: 0.8070 (t80) cc_final: 0.7593 (t80) REVERT: H 355 MET cc_start: 0.6534 (pmm) cc_final: 0.6039 (pmm) REVERT: H 356 TRP cc_start: 0.7540 (m100) cc_final: 0.6763 (m100) REVERT: I 50 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7761 (mmmt) REVERT: I 59 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7746 (tp40) REVERT: I 82 MET cc_start: 0.8343 (mmt) cc_final: 0.7911 (mmm) REVERT: I 154 ASP cc_start: 0.8184 (t70) cc_final: 0.7270 (t70) REVERT: I 178 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7650 (tt) REVERT: I 207 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7642 (mm-30) REVERT: I 280 ASN cc_start: 0.7186 (m-40) cc_final: 0.6905 (m110) REVERT: I 314 GLN cc_start: 0.6420 (tp40) cc_final: 0.6117 (tp40) REVERT: I 325 MET cc_start: 0.6647 (ppp) cc_final: 0.5806 (ppp) outliers start: 164 outliers final: 117 residues processed: 685 average time/residue: 0.2451 time to fit residues: 274.3608 Evaluate side-chains 661 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 535 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 241 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 383 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 chunk 479 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 192 HIS B 83 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Q 59 GLN R 12 ASN R 59 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 275 HIS ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 263 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090563 restraints weight = 87297.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092808 restraints weight = 44164.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094249 restraints weight = 27597.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095197 restraints weight = 20094.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095786 restraints weight = 16282.634| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40029 Z= 0.144 Angle : 0.655 12.162 54328 Z= 0.324 Chirality : 0.046 0.231 6016 Planarity : 0.005 0.064 6988 Dihedral : 8.091 162.994 5514 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.13 % Allowed : 19.95 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 4875 helix: 0.77 (0.12), residues: 1840 sheet: -0.70 (0.17), residues: 953 loop : -0.48 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 138 TYR 0.030 0.001 TYR D 65 PHE 0.018 0.001 PHE D 127 TRP 0.051 0.002 TRP G 129 HIS 0.005 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (40028) covalent geometry : angle 0.65444 / 0.32 (54326) SS BOND : bond 0.01054 / 0.55 ( 1) SS BOND : angle 2.13306 / 1.42 ( 2) hydrogen bonds : bond 0.03981 / 2.72 ( 1733) hydrogen bonds : angle 5.03246 / 3.56 ( 4749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 578 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5290 (OUTLIER) cc_final: 0.3834 (m-80) REVERT: A 83 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7397 (ttmm) REVERT: A 95 ARG cc_start: 0.7405 (ptp-170) cc_final: 0.7016 (ptp-170) REVERT: A 214 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6816 (ttm170) REVERT: A 264 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6583 (mpt180) REVERT: A 281 ASP cc_start: 0.8016 (t0) cc_final: 0.7677 (t0) REVERT: B 19 TYR cc_start: 0.7610 (m-80) cc_final: 0.7227 (m-10) REVERT: B 64 LEU cc_start: 0.8000 (mp) cc_final: 0.7798 (mt) REVERT: B 107 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: B 133 TYR cc_start: 0.8261 (t80) cc_final: 0.7212 (t80) REVERT: B 227 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: B 277 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7408 (t80) REVERT: B 283 GLN cc_start: 0.7913 (tp40) cc_final: 0.7433 (mm110) REVERT: B 320 LEU cc_start: 0.8200 (tp) cc_final: 0.7843 (tp) REVERT: B 324 ARG cc_start: 0.6978 (tpp80) cc_final: 0.6607 (tpp80) REVERT: C 131 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 286 HIS cc_start: 0.7998 (t70) cc_final: 0.7479 (t70) REVERT: D 129 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7878 (mmtp) REVERT: D 280 MET cc_start: 0.8721 (mmt) cc_final: 0.8362 (mmp) REVERT: E 61 GLU cc_start: 0.5514 (tp30) cc_final: 0.5215 (tp30) REVERT: E 76 PHE cc_start: 0.6362 (t80) cc_final: 0.5974 (t80) REVERT: E 83 ARG cc_start: 0.5693 (tpp80) cc_final: 0.5334 (tpp80) REVERT: E 97 ASN cc_start: 0.7842 (m-40) cc_final: 0.7445 (m-40) REVERT: E 98 SER cc_start: 0.8542 (t) cc_final: 0.7849 (p) REVERT: E 159 LYS cc_start: 0.6812 (pttm) cc_final: 0.6522 (ttpp) REVERT: F 137 GLU cc_start: 0.7555 (tp30) cc_final: 0.7055 (tp30) REVERT: G 22 PHE cc_start: 0.8348 (m-80) cc_final: 0.8083 (m-80) REVERT: G 82 ASP cc_start: 0.8275 (m-30) cc_final: 0.8014 (m-30) REVERT: M 122 ILE cc_start: 0.8437 (mt) cc_final: 0.8198 (mm) REVERT: M 123 MET cc_start: 0.7711 (tpp) cc_final: 0.7118 (ttm) REVERT: N 41 GLN cc_start: 0.4734 (pm20) cc_final: 0.4410 (pm20) REVERT: N 44 MET cc_start: 0.5311 (tpt) cc_final: 0.4430 (mtm) REVERT: N 94 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8601 (mm) REVERT: O 206 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7787 (ttp80) REVERT: O 337 TYR cc_start: 0.7943 (m-80) cc_final: 0.7646 (m-80) REVERT: P 64 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8759 (mp) REVERT: P 68 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8182 (mtpp) REVERT: P 69 TYR cc_start: 0.8183 (m-80) cc_final: 0.7962 (m-80) REVERT: P 227 MET cc_start: 0.8795 (mmm) cc_final: 0.8527 (mmt) REVERT: Q 47 MET cc_start: 0.6706 (mmm) cc_final: 0.5858 (ptp) REVERT: Q 176 MET cc_start: 0.7931 (mmm) cc_final: 0.7718 (mmt) REVERT: Q 283 MET cc_start: 0.8503 (mmm) cc_final: 0.8119 (mmt) REVERT: R 94 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7741 (mp) REVERT: R 269 MET cc_start: 0.8137 (ttm) cc_final: 0.7728 (ttm) REVERT: R 276 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7517 (mt-10) REVERT: H 140 LEU cc_start: 0.8780 (mt) cc_final: 0.8555 (mp) REVERT: H 249 THR cc_start: 0.8147 (m) cc_final: 0.7764 (p) REVERT: H 286 ASP cc_start: 0.7279 (p0) cc_final: 0.6422 (p0) REVERT: H 290 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6804 (mtm180) REVERT: H 294 TYR cc_start: 0.7028 (m-80) cc_final: 0.6428 (m-10) REVERT: H 313 MET cc_start: 0.8113 (tpt) cc_final: 0.7259 (tpp) REVERT: H 352 PHE cc_start: 0.7726 (t80) cc_final: 0.7517 (t80) REVERT: H 355 MET cc_start: 0.6880 (pmm) cc_final: 0.6412 (pmm) REVERT: I 45 VAL cc_start: 0.6613 (OUTLIER) cc_final: 0.6382 (t) REVERT: I 50 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7752 (mmmt) REVERT: I 59 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7568 (tp40) REVERT: I 82 MET cc_start: 0.8379 (mmt) cc_final: 0.7950 (mmm) REVERT: I 120 THR cc_start: 0.7454 (m) cc_final: 0.7251 (p) REVERT: I 207 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7419 (mm-30) REVERT: I 227 MET cc_start: 0.7988 (ttt) cc_final: 0.7628 (mtp) REVERT: I 263 GLN cc_start: 0.8138 (mt0) cc_final: 0.7783 (mt0) REVERT: I 280 ASN cc_start: 0.7309 (m-40) cc_final: 0.6968 (m110) REVERT: I 314 GLN cc_start: 0.6495 (tp40) cc_final: 0.6201 (tp40) REVERT: I 316 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7394 (mm-30) REVERT: I 325 MET cc_start: 0.6423 (ppp) cc_final: 0.5765 (ppp) outliers start: 132 outliers final: 91 residues processed: 674 average time/residue: 0.2534 time to fit residues: 277.1562 Evaluate side-chains 650 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 549 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 19 optimal weight: 3.9990 chunk 478 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 473 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN G 51 ASN Q 59 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089540 restraints weight = 86175.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091777 restraints weight = 43736.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.093239 restraints weight = 27318.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094153 restraints weight = 19835.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094672 restraints weight = 16064.268| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40029 Z= 0.173 Angle : 0.662 11.904 54328 Z= 0.327 Chirality : 0.046 0.205 6016 Planarity : 0.005 0.056 6988 Dihedral : 7.949 161.576 5514 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.25 % Allowed : 20.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4875 helix: 0.81 (0.12), residues: 1841 sheet: -0.62 (0.17), residues: 943 loop : -0.44 (0.15), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 167 TYR 0.027 0.001 TYR G 112 PHE 0.018 0.001 PHE D 250 TRP 0.035 0.002 TRP E 160 HIS 0.006 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (40028) covalent geometry : angle 0.66227 / 0.33 (54326) SS BOND : bond 0.01209 / 0.64 ( 1) SS BOND : angle 2.42475 / 1.62 ( 2) hydrogen bonds : bond 0.03983 / 2.72 ( 1733) hydrogen bonds : angle 4.99654 / 3.53 ( 4749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 566 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.3993 (m-80) REVERT: A 83 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7381 (ttmm) REVERT: A 214 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6848 (ttm170) REVERT: A 264 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6444 (mpt180) REVERT: B 19 TYR cc_start: 0.7603 (m-80) cc_final: 0.7221 (m-10) REVERT: B 64 LEU cc_start: 0.7881 (mp) cc_final: 0.7662 (mt) REVERT: B 82 MET cc_start: 0.8162 (tpt) cc_final: 0.7837 (tpt) REVERT: B 107 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: B 133 TYR cc_start: 0.8146 (t80) cc_final: 0.7355 (t80) REVERT: B 159 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7485 (m) REVERT: B 227 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7281 (t-90) REVERT: B 277 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 283 GLN cc_start: 0.7979 (tp40) cc_final: 0.7485 (mm110) REVERT: B 320 LEU cc_start: 0.8247 (tp) cc_final: 0.7883 (tp) REVERT: B 324 ARG cc_start: 0.6984 (tpp80) cc_final: 0.6613 (tpp80) REVERT: C 91 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8001 (ttpp) REVERT: C 131 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 286 HIS cc_start: 0.8028 (t70) cc_final: 0.7504 (t70) REVERT: D 113 MET cc_start: 0.7933 (tpp) cc_final: 0.7410 (mmt) REVERT: D 280 MET cc_start: 0.8796 (mmt) cc_final: 0.8423 (mmp) REVERT: E 97 ASN cc_start: 0.7864 (m-40) cc_final: 0.7488 (m-40) REVERT: E 98 SER cc_start: 0.8548 (t) cc_final: 0.7856 (p) REVERT: F 86 LEU cc_start: 0.8892 (mm) cc_final: 0.8680 (mm) REVERT: F 137 GLU cc_start: 0.7510 (tp30) cc_final: 0.7023 (tp30) REVERT: G 22 PHE cc_start: 0.8349 (m-80) cc_final: 0.8093 (m-80) REVERT: G 82 ASP cc_start: 0.8289 (m-30) cc_final: 0.8031 (m-30) REVERT: M 117 GLU cc_start: 0.7449 (mp0) cc_final: 0.7072 (mp0) REVERT: M 122 ILE cc_start: 0.8475 (mt) cc_final: 0.8209 (mm) REVERT: M 123 MET cc_start: 0.7697 (tpp) cc_final: 0.7170 (ttm) REVERT: N 41 GLN cc_start: 0.4679 (pm20) cc_final: 0.4381 (pm20) REVERT: N 44 MET cc_start: 0.5042 (tpt) cc_final: 0.4352 (mtm) REVERT: N 94 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8594 (mm) REVERT: O 206 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7805 (ttp80) REVERT: O 337 TYR cc_start: 0.7969 (m-80) cc_final: 0.7662 (m-80) REVERT: P 64 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8741 (mp) REVERT: P 68 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: P 69 TYR cc_start: 0.8215 (m-80) cc_final: 0.7995 (m-80) REVERT: P 227 MET cc_start: 0.8808 (mmm) cc_final: 0.8137 (mmt) REVERT: Q 47 MET cc_start: 0.6872 (mmm) cc_final: 0.5953 (ptp) REVERT: Q 283 MET cc_start: 0.8516 (mmm) cc_final: 0.8121 (mmt) REVERT: R 269 MET cc_start: 0.8153 (ttm) cc_final: 0.7805 (ttm) REVERT: R 276 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7679 (mt-10) REVERT: H 140 LEU cc_start: 0.8693 (mt) cc_final: 0.8436 (mp) REVERT: H 249 THR cc_start: 0.8170 (m) cc_final: 0.7797 (p) REVERT: H 286 ASP cc_start: 0.7319 (p0) cc_final: 0.6446 (p0) REVERT: H 290 ARG cc_start: 0.7362 (mtm180) cc_final: 0.6807 (mtm180) REVERT: H 294 TYR cc_start: 0.7031 (m-80) cc_final: 0.6422 (m-10) REVERT: H 352 PHE cc_start: 0.7718 (t80) cc_final: 0.7499 (t80) REVERT: H 355 MET cc_start: 0.6922 (pmm) cc_final: 0.6467 (pmm) REVERT: I 50 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7760 (mmmt) REVERT: I 59 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7434 (tp40) REVERT: I 82 MET cc_start: 0.8402 (mmt) cc_final: 0.7969 (mmm) REVERT: I 120 THR cc_start: 0.7517 (m) cc_final: 0.7315 (p) REVERT: I 207 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7384 (mm-30) REVERT: I 244 ASP cc_start: 0.7225 (p0) cc_final: 0.6992 (p0) REVERT: I 280 ASN cc_start: 0.7283 (m-40) cc_final: 0.6945 (m110) REVERT: I 314 GLN cc_start: 0.6542 (tp40) cc_final: 0.6265 (tp40) REVERT: I 325 MET cc_start: 0.6424 (ppp) cc_final: 0.5779 (ppp) outliers start: 137 outliers final: 106 residues processed: 669 average time/residue: 0.2350 time to fit residues: 256.8498 Evaluate side-chains 665 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 549 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 100 GLU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 266 PHE Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 137 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 422 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 403 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS B 48 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN F 129 HIS O 49 GLN O 275 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 263 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090055 restraints weight = 86289.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092301 restraints weight = 43764.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093751 restraints weight = 27280.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094697 restraints weight = 19813.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095299 restraints weight = 16033.582| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40029 Z= 0.155 Angle : 0.656 12.086 54328 Z= 0.323 Chirality : 0.046 0.209 6016 Planarity : 0.005 0.053 6988 Dihedral : 7.787 158.774 5514 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.32 % Allowed : 20.83 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4875 helix: 0.85 (0.12), residues: 1843 sheet: -0.57 (0.17), residues: 943 loop : -0.41 (0.15), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 167 TYR 0.027 0.001 TYR G 112 PHE 0.018 0.001 PHE D 250 TRP 0.030 0.002 TRP G 129 HIS 0.006 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (40028) covalent geometry : angle 0.65563 / 0.32 (54326) SS BOND : bond 0.00683 / 0.36 ( 1) SS BOND : angle 2.36662 / 1.58 ( 2) hydrogen bonds : bond 0.03847 / 2.63 ( 1733) hydrogen bonds : angle 4.94857 / 3.50 ( 4749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 574 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.3992 (m-80) REVERT: A 83 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7373 (ttmm) REVERT: A 214 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6811 (ttm170) REVERT: A 264 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6520 (mpt180) REVERT: B 19 TYR cc_start: 0.7574 (m-80) cc_final: 0.7054 (m-10) REVERT: B 64 LEU cc_start: 0.7830 (mp) cc_final: 0.7613 (mt) REVERT: B 107 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 133 TYR cc_start: 0.8151 (t80) cc_final: 0.7439 (t80) REVERT: B 227 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7266 (t-90) REVERT: B 277 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 283 GLN cc_start: 0.7972 (tp40) cc_final: 0.7465 (mm110) REVERT: B 320 LEU cc_start: 0.8235 (tp) cc_final: 0.7858 (tp) REVERT: B 324 ARG cc_start: 0.6995 (tpp80) cc_final: 0.6631 (tpp80) REVERT: C 131 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 286 HIS cc_start: 0.8019 (t70) cc_final: 0.7456 (t70) REVERT: D 113 MET cc_start: 0.7954 (tpp) cc_final: 0.7393 (mmt) REVERT: D 280 MET cc_start: 0.8783 (mmm) cc_final: 0.8427 (mmp) REVERT: E 76 PHE cc_start: 0.6341 (t80) cc_final: 0.5973 (t80) REVERT: E 79 GLU cc_start: 0.6038 (tp30) cc_final: 0.4908 (tp30) REVERT: E 83 ARG cc_start: 0.5476 (tpp80) cc_final: 0.5227 (tpp80) REVERT: E 97 ASN cc_start: 0.7815 (m-40) cc_final: 0.7435 (m-40) REVERT: E 98 SER cc_start: 0.8497 (t) cc_final: 0.7868 (p) REVERT: F 86 LEU cc_start: 0.8887 (mm) cc_final: 0.8677 (mm) REVERT: F 124 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7117 (tt0) REVERT: F 137 GLU cc_start: 0.7486 (tp30) cc_final: 0.6997 (tp30) REVERT: G 22 PHE cc_start: 0.8340 (m-80) cc_final: 0.8081 (m-80) REVERT: G 82 ASP cc_start: 0.8272 (m-30) cc_final: 0.7998 (m-30) REVERT: M 117 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: M 122 ILE cc_start: 0.8485 (mt) cc_final: 0.8225 (mm) REVERT: M 123 MET cc_start: 0.7647 (tpp) cc_final: 0.7133 (ttm) REVERT: N 44 MET cc_start: 0.5029 (tpt) cc_final: 0.4379 (mtm) REVERT: N 94 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8645 (mm) REVERT: N 123 MET cc_start: 0.7911 (ttm) cc_final: 0.7464 (mtp) REVERT: O 206 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7808 (ttp80) REVERT: O 337 TYR cc_start: 0.7906 (m-80) cc_final: 0.7585 (m-80) REVERT: P 64 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8804 (mp) REVERT: P 68 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8167 (mtpp) REVERT: P 69 TYR cc_start: 0.8210 (m-80) cc_final: 0.7997 (m-80) REVERT: P 227 MET cc_start: 0.8795 (mmm) cc_final: 0.8142 (mmt) REVERT: Q 47 MET cc_start: 0.6837 (mmm) cc_final: 0.5802 (ptp) REVERT: Q 283 MET cc_start: 0.8515 (mmm) cc_final: 0.8121 (mmt) REVERT: R 269 MET cc_start: 0.8149 (ttm) cc_final: 0.7815 (ttm) REVERT: R 276 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7594 (mt-10) REVERT: H 140 LEU cc_start: 0.8667 (mt) cc_final: 0.8378 (mp) REVERT: H 249 THR cc_start: 0.8147 (m) cc_final: 0.7776 (p) REVERT: H 260 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7859 (p) REVERT: H 294 TYR cc_start: 0.6987 (m-80) cc_final: 0.6261 (m-10) REVERT: H 352 PHE cc_start: 0.7604 (t80) cc_final: 0.7374 (t80) REVERT: H 355 MET cc_start: 0.6906 (pmm) cc_final: 0.6458 (pmm) REVERT: I 50 LYS cc_start: 0.8115 (mmpt) cc_final: 0.7761 (mmmt) REVERT: I 59 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7714 (tp40) REVERT: I 82 MET cc_start: 0.8389 (mmt) cc_final: 0.7956 (mmm) REVERT: I 207 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7574 (mm-30) REVERT: I 241 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7314 (tm-30) REVERT: I 263 GLN cc_start: 0.8001 (mt0) cc_final: 0.7796 (mt0) REVERT: I 280 ASN cc_start: 0.7267 (m-40) cc_final: 0.6937 (m110) REVERT: I 314 GLN cc_start: 0.6532 (tp40) cc_final: 0.6277 (tp40) REVERT: I 316 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7406 (mm-30) REVERT: I 325 MET cc_start: 0.6292 (ppp) cc_final: 0.5684 (ppp) outliers start: 140 outliers final: 109 residues processed: 678 average time/residue: 0.2424 time to fit residues: 267.8682 Evaluate side-chains 670 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 551 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 266 PHE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 391 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 374 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 283 optimal weight: 0.0970 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 352 optimal weight: 0.7980 chunk 330 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN G 38 GLN G 42 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090872 restraints weight = 86434.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093137 restraints weight = 43630.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094600 restraints weight = 27210.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095546 restraints weight = 19755.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096114 restraints weight = 15961.129| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40029 Z= 0.136 Angle : 0.648 12.206 54328 Z= 0.319 Chirality : 0.045 0.217 6016 Planarity : 0.004 0.058 6988 Dihedral : 7.630 157.590 5514 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.08 % Allowed : 20.83 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4875 helix: 0.91 (0.12), residues: 1843 sheet: -0.49 (0.17), residues: 941 loop : -0.34 (0.15), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 167 TYR 0.029 0.001 TYR G 112 PHE 0.021 0.001 PHE D 127 TRP 0.037 0.002 TRP E 160 HIS 0.006 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (40028) covalent geometry : angle 0.64795 / 0.32 (54326) SS BOND : bond 0.00629 / 0.33 ( 1) SS BOND : angle 2.26494 / 1.51 ( 2) hydrogen bonds : bond 0.03686 / 2.53 ( 1733) hydrogen bonds : angle 4.90136 / 3.46 ( 4749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 580 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.3953 (m-80) REVERT: A 83 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7352 (ttmm) REVERT: A 194 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8800 (mm) REVERT: A 214 ARG cc_start: 0.7013 (ttm170) cc_final: 0.6751 (ttm170) REVERT: B 19 TYR cc_start: 0.7556 (m-80) cc_final: 0.7068 (m-10) REVERT: B 107 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: B 227 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: B 277 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 283 GLN cc_start: 0.7895 (tp40) cc_final: 0.7375 (mm110) REVERT: B 320 LEU cc_start: 0.8261 (tp) cc_final: 0.7894 (tp) REVERT: B 324 ARG cc_start: 0.7004 (tpp80) cc_final: 0.6726 (tpp80) REVERT: C 286 HIS cc_start: 0.8009 (t70) cc_final: 0.7469 (t70) REVERT: D 64 ASN cc_start: 0.8170 (t0) cc_final: 0.7595 (m-40) REVERT: D 280 MET cc_start: 0.8743 (mmm) cc_final: 0.8402 (mmp) REVERT: E 76 PHE cc_start: 0.6306 (t80) cc_final: 0.5942 (t80) REVERT: E 97 ASN cc_start: 0.7834 (m-40) cc_final: 0.7457 (m-40) REVERT: E 98 SER cc_start: 0.8566 (t) cc_final: 0.7803 (p) REVERT: F 86 LEU cc_start: 0.8882 (mm) cc_final: 0.8667 (mm) REVERT: G 22 PHE cc_start: 0.8332 (m-80) cc_final: 0.8071 (m-80) REVERT: G 82 ASP cc_start: 0.8275 (m-30) cc_final: 0.8012 (m-30) REVERT: M 117 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: M 122 ILE cc_start: 0.8480 (mt) cc_final: 0.8207 (mm) REVERT: M 123 MET cc_start: 0.7596 (tpp) cc_final: 0.7109 (ttm) REVERT: N 41 GLN cc_start: 0.4649 (pm20) cc_final: 0.4375 (pm20) REVERT: N 44 MET cc_start: 0.5215 (tpt) cc_final: 0.4358 (mtm) REVERT: N 94 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8668 (mm) REVERT: O 206 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7795 (ttp80) REVERT: O 325 MET cc_start: 0.7236 (ptp) cc_final: 0.7025 (ptp) REVERT: O 337 TYR cc_start: 0.7829 (m-80) cc_final: 0.7486 (m-80) REVERT: P 64 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8717 (mp) REVERT: P 68 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: P 69 TYR cc_start: 0.8214 (m-80) cc_final: 0.7997 (m-80) REVERT: P 227 MET cc_start: 0.8784 (mmm) cc_final: 0.8128 (mmt) REVERT: Q 47 MET cc_start: 0.6799 (mmm) cc_final: 0.5753 (ptp) REVERT: Q 176 MET cc_start: 0.7864 (mmm) cc_final: 0.7642 (mmt) REVERT: Q 283 MET cc_start: 0.8516 (mmm) cc_final: 0.8155 (mmp) REVERT: R 269 MET cc_start: 0.8157 (ttm) cc_final: 0.7825 (ttm) REVERT: R 276 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7499 (mt-10) REVERT: H 140 LEU cc_start: 0.8648 (mt) cc_final: 0.8351 (mp) REVERT: H 249 THR cc_start: 0.8120 (m) cc_final: 0.7756 (p) REVERT: H 260 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7866 (p) REVERT: H 294 TYR cc_start: 0.6941 (m-80) cc_final: 0.6303 (m-10) REVERT: H 352 PHE cc_start: 0.7549 (t80) cc_final: 0.7338 (t80) REVERT: H 355 MET cc_start: 0.7052 (pmm) cc_final: 0.6601 (pmm) REVERT: I 50 LYS cc_start: 0.8111 (mmpt) cc_final: 0.7761 (mmmt) REVERT: I 59 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7665 (tp40) REVERT: I 82 MET cc_start: 0.8404 (mmt) cc_final: 0.7963 (mmm) REVERT: I 207 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7562 (mm-30) REVERT: I 241 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7312 (tm-30) REVERT: I 280 ASN cc_start: 0.7269 (m-40) cc_final: 0.6925 (m110) REVERT: I 293 LEU cc_start: 0.7365 (mm) cc_final: 0.7031 (mm) REVERT: I 316 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7402 (mm-30) REVERT: I 325 MET cc_start: 0.6283 (ppp) cc_final: 0.5686 (ppp) outliers start: 130 outliers final: 105 residues processed: 672 average time/residue: 0.2499 time to fit residues: 274.0272 Evaluate side-chains 667 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 552 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 266 PHE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 444 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 476 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 438 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 442 optimal weight: 0.9990 chunk 482 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN F 58 GLN M 101 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN H 297 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091249 restraints weight = 85791.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093509 restraints weight = 43410.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094969 restraints weight = 27075.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095903 restraints weight = 19671.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096493 restraints weight = 15924.839| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40029 Z= 0.131 Angle : 0.654 15.872 54328 Z= 0.320 Chirality : 0.045 0.246 6016 Planarity : 0.004 0.062 6988 Dihedral : 7.531 157.371 5514 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.80 % Allowed : 21.38 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4875 helix: 0.95 (0.12), residues: 1844 sheet: -0.47 (0.17), residues: 941 loop : -0.30 (0.15), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 167 TYR 0.030 0.001 TYR G 112 PHE 0.020 0.001 PHE D 250 TRP 0.027 0.002 TRP G 129 HIS 0.006 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (40028) covalent geometry : angle 0.65371 / 0.32 (54326) SS BOND : bond 0.00541 / 0.28 ( 1) SS BOND : angle 2.20262 / 1.47 ( 2) hydrogen bonds : bond 0.03600 / 2.47 ( 1733) hydrogen bonds : angle 4.86637 / 3.44 ( 4749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 579 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.3941 (m-80) REVERT: A 83 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7344 (ttmm) REVERT: A 194 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 19 TYR cc_start: 0.7570 (m-80) cc_final: 0.7066 (m-10) REVERT: B 107 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 227 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: B 277 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 283 GLN cc_start: 0.7859 (tp40) cc_final: 0.7349 (mm110) REVERT: B 320 LEU cc_start: 0.8262 (tp) cc_final: 0.7900 (tp) REVERT: B 324 ARG cc_start: 0.7011 (tpp80) cc_final: 0.6734 (tpp80) REVERT: C 286 HIS cc_start: 0.8002 (t70) cc_final: 0.7474 (t70) REVERT: D 64 ASN cc_start: 0.8168 (t0) cc_final: 0.7591 (m-40) REVERT: D 280 MET cc_start: 0.8799 (mmm) cc_final: 0.8449 (mmp) REVERT: E 76 PHE cc_start: 0.6280 (t80) cc_final: 0.5915 (t80) REVERT: E 83 ARG cc_start: 0.5492 (tpp80) cc_final: 0.5197 (tpp80) REVERT: E 97 ASN cc_start: 0.7874 (m-40) cc_final: 0.7492 (m-40) REVERT: E 98 SER cc_start: 0.8518 (t) cc_final: 0.7815 (p) REVERT: G 22 PHE cc_start: 0.8324 (m-80) cc_final: 0.8060 (m-80) REVERT: G 82 ASP cc_start: 0.8266 (m-30) cc_final: 0.8010 (m-30) REVERT: M 117 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: M 122 ILE cc_start: 0.8480 (mt) cc_final: 0.8219 (mm) REVERT: M 123 MET cc_start: 0.7582 (tpp) cc_final: 0.7107 (ttm) REVERT: N 41 GLN cc_start: 0.4603 (pm20) cc_final: 0.4340 (pm20) REVERT: N 44 MET cc_start: 0.5242 (tpt) cc_final: 0.4591 (mtm) REVERT: N 94 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (mm) REVERT: N 123 MET cc_start: 0.8032 (ttm) cc_final: 0.7534 (mtp) REVERT: O 206 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7802 (ttp80) REVERT: O 337 TYR cc_start: 0.7783 (m-80) cc_final: 0.7423 (m-80) REVERT: O 353 GLN cc_start: 0.8528 (mp10) cc_final: 0.8227 (mp10) REVERT: P 69 TYR cc_start: 0.8212 (m-80) cc_final: 0.7998 (m-80) REVERT: P 83 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7806 (mt-10) REVERT: P 227 MET cc_start: 0.8778 (mmm) cc_final: 0.8116 (mmt) REVERT: Q 47 MET cc_start: 0.6795 (mmm) cc_final: 0.5725 (ptp) REVERT: Q 283 MET cc_start: 0.8522 (mmm) cc_final: 0.8159 (mmp) REVERT: R 269 MET cc_start: 0.8147 (ttm) cc_final: 0.7828 (ttm) REVERT: R 276 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7486 (mt-10) REVERT: H 140 LEU cc_start: 0.8620 (mt) cc_final: 0.8317 (mp) REVERT: H 249 THR cc_start: 0.8107 (m) cc_final: 0.7745 (p) REVERT: H 260 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7859 (p) REVERT: H 294 TYR cc_start: 0.6886 (m-80) cc_final: 0.6264 (m-10) REVERT: H 313 MET cc_start: 0.8043 (tpt) cc_final: 0.7735 (tpp) REVERT: H 352 PHE cc_start: 0.7523 (t80) cc_final: 0.7310 (t80) REVERT: H 355 MET cc_start: 0.7000 (pmm) cc_final: 0.6716 (pmm) REVERT: I 50 LYS cc_start: 0.8108 (mmpt) cc_final: 0.7759 (mmmt) REVERT: I 82 MET cc_start: 0.8395 (mmt) cc_final: 0.7934 (mmm) REVERT: I 207 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7624 (mm-30) REVERT: I 241 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7286 (tm-30) REVERT: I 263 GLN cc_start: 0.8208 (mt0) cc_final: 0.7966 (pt0) REVERT: I 280 ASN cc_start: 0.7171 (m-40) cc_final: 0.6823 (m110) REVERT: I 293 LEU cc_start: 0.7372 (mm) cc_final: 0.7013 (mm) REVERT: I 314 GLN cc_start: 0.6612 (tp40) cc_final: 0.6278 (tp40) REVERT: I 316 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7413 (mm-30) REVERT: I 325 MET cc_start: 0.6252 (ppp) cc_final: 0.5667 (ppp) outliers start: 118 outliers final: 105 residues processed: 660 average time/residue: 0.2495 time to fit residues: 269.3271 Evaluate side-chains 674 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 561 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 266 PHE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 57 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 403 optimal weight: 2.9990 chunk 472 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 418 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 478 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 249 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 297 ASN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091304 restraints weight = 86368.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093568 restraints weight = 43752.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095029 restraints weight = 27262.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095994 restraints weight = 19809.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096584 restraints weight = 15999.257| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40029 Z= 0.134 Angle : 0.654 15.650 54328 Z= 0.320 Chirality : 0.045 0.241 6016 Planarity : 0.004 0.065 6988 Dihedral : 7.462 156.654 5514 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.92 % Allowed : 21.49 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4875 helix: 0.97 (0.12), residues: 1844 sheet: -0.47 (0.17), residues: 941 loop : -0.29 (0.15), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 116 TYR 0.025 0.001 TYR I 218 PHE 0.020 0.001 PHE D 250 TRP 0.026 0.002 TRP G 129 HIS 0.006 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (40028) covalent geometry : angle 0.65382 / 0.32 (54326) SS BOND : bond 0.00547 / 0.29 ( 1) SS BOND : angle 2.21752 / 1.48 ( 2) hydrogen bonds : bond 0.03577 / 2.45 ( 1733) hydrogen bonds : angle 4.85732 / 3.43 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8262.93 seconds wall clock time: 143 minutes 14.37 seconds (8594.37 seconds total)