Starting phenix.real_space_refine on Tue Aug 26 17:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9b_27962/08_2025/8e9b_27962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9b_27962/08_2025/8e9b_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_27962/08_2025/8e9b_27962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9b_27962/08_2025/8e9b_27962.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9b_27962/08_2025/8e9b_27962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9b_27962/08_2025/8e9b_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.35, per 1000 atoms: 0.21 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: 2.94 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.58 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: 10.28 Time building geometry restraints manager: 3.93 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: 23443 33.36 - 66.73: 587 66.73 - 100.09: 57 100.09 - 133.45: 4 133.45 - 166.82: 8 Dihedral angle restraints: 24099 sinusoidal: 9778 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 24096 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: 2.370 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.300 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 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: 0.020 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: 41.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 15.386 166.817 14894 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 aren 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 covalent geometry : bond 0.00363 (40028) covalent geometry : angle 0.70740 (54326) SS BOND : bond 0.78963 ( 1) SS BOND : angle 24.93740 ( 2) hydrogen bonds : bond 0.18236 ( 1733) hydrogen bonds : angle 6.72096 ( 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 : 0.994 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: 0.8072 (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: 0.2202 time to fit residues: 442.6378 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 : 1.385 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 150 GLN 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 173 HIS H 246 GLN H 297 ASN H 371 HIS ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089878 restraints weight = 88763.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091998 restraints weight = 46186.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093396 restraints weight = 29465.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094298 restraints weight = 21738.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094852 restraints weight = 17750.836| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.152 40029 Z= 0.319 Angle : 0.803 15.388 54328 Z= 0.407 Chirality : 0.051 0.184 6016 Planarity : 0.006 0.163 6988 Dihedral : 9.194 172.539 5548 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 2.35 % Allowed : 14.14 % Favored : 83.51 % 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 aren not related in a simple way. whole: -0.37 (0.12), residues: 4875 helix: 0.57 (0.12), residues: 1831 sheet: -0.83 (0.17), residues: 967 loop : -0.54 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG I 116 TYR 0.028 0.002 TYR R 166 PHE 0.027 0.003 PHE A 150 TRP 0.055 0.003 TRP Q 340 HIS 0.009 0.002 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00752 (40028) covalent geometry : angle 0.80333 (54326) SS BOND : bond 0.01145 ( 1) SS BOND : angle 2.29649 ( 2) hydrogen bonds : bond 0.05202 ( 1733) hydrogen bonds : angle 5.57703 ( 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 794 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 695 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5240 (m-80) cc_final: 0.4559 (m-80) REVERT: A 95 ARG cc_start: 0.7406 (ptp-110) cc_final: 0.7189 (ptp-170) REVERT: A 133 LEU cc_start: 0.7574 (mp) cc_final: 0.7176 (tp) REVERT: A 140 GLU cc_start: 0.8273 (tt0) cc_final: 0.8071 (pt0) REVERT: A 234 LEU cc_start: 0.8147 (tt) cc_final: 0.7924 (tp) REVERT: A 295 ASN cc_start: 0.8318 (t0) cc_final: 0.7909 (t0) REVERT: A 368 LYS cc_start: 0.7922 (pptt) cc_final: 0.6817 (mmtm) REVERT: A 382 GLN cc_start: 0.8412 (mm110) cc_final: 0.8119 (tp-100) REVERT: A 420 TYR cc_start: 0.5026 (t80) cc_final: 0.4626 (t80) REVERT: B 19 TYR cc_start: 0.7704 (m-80) cc_final: 0.7286 (m-10) REVERT: B 81 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7350 (mt-10) REVERT: B 107 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: B 133 TYR cc_start: 0.8105 (t80) cc_final: 0.7137 (t80) REVERT: B 227 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: B 237 MET cc_start: 0.8101 (mmm) cc_final: 0.7831 (mmt) REVERT: B 283 GLN cc_start: 0.8023 (tp40) cc_final: 0.7608 (mm110) REVERT: B 305 MET cc_start: 0.8787 (mmm) cc_final: 0.8494 (mmt) REVERT: B 324 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6557 (tpp80) REVERT: B 329 ASP cc_start: 0.7798 (t0) cc_final: 0.7562 (m-30) REVERT: C 83 GLU cc_start: 0.6340 (pm20) cc_final: 0.5708 (pm20) REVERT: D 109 MET cc_start: 0.8831 (tpp) cc_final: 0.8361 (tpp) REVERT: D 129 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7731 (mmtp) REVERT: D 148 ASP cc_start: 0.6008 (m-30) cc_final: 0.5703 (m-30) REVERT: D 155 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6784 (mm-30) REVERT: E 79 GLU cc_start: 0.6028 (tp30) cc_final: 0.5339 (tp30) REVERT: E 83 ARG cc_start: 0.4831 (tpp80) cc_final: 0.4543 (tpp80) REVERT: E 97 ASN cc_start: 0.7865 (m-40) cc_final: 0.7401 (m-40) REVERT: E 98 SER cc_start: 0.7933 (t) cc_final: 0.7496 (p) REVERT: F 9 LEU cc_start: 0.8168 (mt) cc_final: 0.7938 (mt) REVERT: F 89 LYS cc_start: 0.8127 (tppp) cc_final: 0.7899 (ttpt) REVERT: F 137 GLU cc_start: 0.7515 (tp30) cc_final: 0.6876 (tp30) REVERT: G 27 GLU cc_start: 0.7771 (tt0) cc_final: 0.7500 (tt0) REVERT: G 82 ASP cc_start: 0.8158 (m-30) cc_final: 0.7894 (m-30) REVERT: G 97 LYS cc_start: 0.6360 (pptt) cc_final: 0.6145 (pttp) REVERT: G 151 ASP cc_start: 0.6469 (p0) cc_final: 0.5961 (p0) REVERT: M 122 ILE cc_start: 0.8360 (mt) cc_final: 0.8138 (mm) REVERT: M 123 MET cc_start: 0.8008 (tpt) cc_final: 0.7701 (tpp) REVERT: N 44 MET cc_start: 0.5222 (tpt) cc_final: 0.4678 (mtm) REVERT: O 132 MET cc_start: 0.7332 (ppp) cc_final: 0.7013 (ppp) REVERT: O 206 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7801 (ttp80) REVERT: O 283 MET cc_start: 0.9027 (mmm) cc_final: 0.8782 (mmm) REVERT: O 337 TYR cc_start: 0.7965 (m-80) cc_final: 0.7682 (m-80) REVERT: P 69 TYR cc_start: 0.8329 (m-80) cc_final: 0.8041 (m-80) REVERT: P 89 THR cc_start: 0.8396 (m) cc_final: 0.8148 (p) REVERT: P 121 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8305 (tm-30) REVERT: Q 47 MET cc_start: 0.6888 (mmm) cc_final: 0.5915 (ptp) REVERT: Q 283 MET cc_start: 0.8437 (mmm) cc_final: 0.8002 (mmp) REVERT: R 269 MET cc_start: 0.8199 (ttm) cc_final: 0.7964 (ttm) REVERT: H 121 GLN cc_start: 0.8189 (tm130) cc_final: 0.7926 (tm-30) REVERT: H 123 MET cc_start: 0.7839 (ttm) cc_final: 0.7422 (ttm) REVERT: H 140 LEU cc_start: 0.8743 (mt) cc_final: 0.8472 (mp) REVERT: H 236 LEU cc_start: 0.7914 (pt) cc_final: 0.7429 (mt) REVERT: H 237 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6743 (tm-30) REVERT: H 238 LYS cc_start: 0.7107 (mmmm) cc_final: 0.6486 (mptt) REVERT: H 249 THR cc_start: 0.8067 (m) cc_final: 0.7666 (p) REVERT: H 288 ASP cc_start: 0.3871 (t0) cc_final: 0.3669 (t0) REVERT: H 299 MET cc_start: 0.6603 (mtp) cc_final: 0.6320 (mtp) REVERT: H 305 MET cc_start: 0.6149 (tpp) cc_final: 0.5778 (tpt) REVERT: H 311 ASP cc_start: 0.7445 (m-30) cc_final: 0.7107 (m-30) REVERT: H 325 MET cc_start: 0.7299 (mmt) cc_final: 0.6891 (tpp) REVERT: H 329 ILE cc_start: 0.8155 (mm) cc_final: 0.7688 (mt) REVERT: H 352 PHE cc_start: 0.7774 (t80) cc_final: 0.6873 (t80) REVERT: H 355 MET cc_start: 0.7151 (pmm) cc_final: 0.6945 (pmm) REVERT: H 356 TRP cc_start: 0.7598 (m100) cc_final: 0.6774 (m100) REVERT: I 79 TRP cc_start: 0.6215 (m100) cc_final: 0.5719 (m100) REVERT: I 82 MET cc_start: 0.8166 (mmt) cc_final: 0.7798 (mmm) REVERT: I 173 HIS cc_start: 0.5969 (m170) cc_final: 0.5695 (m170) REVERT: I 207 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7767 (mm-30) REVERT: I 222 ASP cc_start: 0.6342 (p0) cc_final: 0.5743 (p0) REVERT: I 241 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7154 (tm-30) REVERT: I 263 GLN cc_start: 0.8350 (mt0) cc_final: 0.8093 (tt0) REVERT: I 280 ASN cc_start: 0.7532 (m-40) cc_final: 0.7051 (m110) REVERT: I 325 MET cc_start: 0.6681 (ppp) cc_final: 0.5933 (ppp) outliers start: 99 outliers final: 68 residues processed: 761 average time/residue: 0.2085 time to fit residues: 255.3582 Evaluate side-chains 653 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 583 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 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 64 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 152 VAL 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 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: 0.8980 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 233 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 470 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 476 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 ASN N 161 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 173 HIS H 246 GLN H 297 ASN I 111 ASN I 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092705 restraints weight = 87587.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094935 restraints weight = 44431.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096414 restraints weight = 27921.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097354 restraints weight = 20346.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097938 restraints weight = 16512.467| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3056 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= 0.132 Angle : 0.637 13.670 54328 Z= 0.317 Chirality : 0.045 0.188 6016 Planarity : 0.004 0.053 6988 Dihedral : 8.813 169.752 5545 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.14 % Allowed : 16.51 % Favored : 81.35 % 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 aren not related in a simple way. whole: -0.04 (0.12), residues: 4875 helix: 0.89 (0.12), residues: 1834 sheet: -0.63 (0.17), residues: 931 loop : -0.44 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 162 TYR 0.024 0.001 TYR D 65 PHE 0.017 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 covalent geometry : bond 0.00296 (40028) covalent geometry : angle 0.63711 (54326) SS BOND : bond 0.01784 ( 1) SS BOND : angle 1.91800 ( 2) hydrogen bonds : bond 0.04006 ( 1733) hydrogen bonds : angle 5.15331 ( 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 746 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 656 time to evaluate : 1.487 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 133 LEU cc_start: 0.7319 (mp) cc_final: 0.6909 (tp) REVERT: A 214 ARG cc_start: 0.6969 (ttm170) cc_final: 0.6513 (mtt180) REVERT: A 281 ASP cc_start: 0.8031 (t0) cc_final: 0.7667 (t0) REVERT: A 295 ASN cc_start: 0.8254 (t0) cc_final: 0.7886 (t0) REVERT: A 368 LYS cc_start: 0.7826 (pptt) cc_final: 0.6744 (mmtm) REVERT: A 382 GLN cc_start: 0.8382 (mm110) cc_final: 0.8068 (tp-100) REVERT: A 420 TYR cc_start: 0.4773 (t80) cc_final: 0.4474 (t80) REVERT: B 19 TYR cc_start: 0.7616 (m-80) cc_final: 0.7058 (m-10) REVERT: B 39 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6998 (mtm180) REVERT: B 81 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 107 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: B 133 TYR cc_start: 0.8046 (t80) cc_final: 0.6971 (t80) REVERT: B 227 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: B 283 GLN cc_start: 0.7896 (tp40) cc_final: 0.7473 (mm110) REVERT: B 305 MET cc_start: 0.8789 (mmm) cc_final: 0.8437 (mmt) REVERT: B 324 ARG cc_start: 0.6934 (tpp80) cc_final: 0.6666 (tpp80) REVERT: B 329 ASP cc_start: 0.7709 (t0) cc_final: 0.7403 (m-30) REVERT: D 109 MET cc_start: 0.8692 (tpp) cc_final: 0.8399 (tpp) REVERT: D 113 MET cc_start: 0.8053 (tpp) cc_final: 0.7456 (mmt) REVERT: D 129 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7813 (mmtp) REVERT: D 205 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7066 (mtm110) REVERT: D 280 MET cc_start: 0.8661 (mmt) cc_final: 0.8243 (mmt) REVERT: E 98 SER cc_start: 0.8218 (t) cc_final: 0.7618 (p) REVERT: E 159 LYS cc_start: 0.6672 (pttm) cc_final: 0.6138 (ttpp) REVERT: F 58 GLN cc_start: 0.8388 (mp-120) cc_final: 0.8187 (mp10) REVERT: F 137 GLU cc_start: 0.7442 (tp30) cc_final: 0.7109 (tp30) REVERT: G 27 GLU cc_start: 0.7761 (tt0) cc_final: 0.7468 (tt0) REVERT: G 82 ASP cc_start: 0.8274 (m-30) cc_final: 0.8020 (m-30) REVERT: M 122 ILE cc_start: 0.8282 (mt) cc_final: 0.7980 (mm) REVERT: M 123 MET cc_start: 0.7890 (tpt) cc_final: 0.7078 (ttm) REVERT: N 44 MET cc_start: 0.5277 (tpt) cc_final: 0.4679 (mtm) REVERT: O 84 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8484 (ttmt) REVERT: O 337 TYR cc_start: 0.7935 (m-80) cc_final: 0.7629 (m-80) REVERT: P 69 TYR cc_start: 0.8322 (m-80) cc_final: 0.8096 (m-80) REVERT: P 227 MET cc_start: 0.8835 (mmm) cc_final: 0.8188 (mmt) REVERT: Q 47 MET cc_start: 0.6618 (mmm) cc_final: 0.5738 (ptp) REVERT: Q 283 MET cc_start: 0.8440 (mmm) cc_final: 0.8107 (mmt) REVERT: R 269 MET cc_start: 0.8067 (ttm) cc_final: 0.7551 (ttm) REVERT: H 92 ASN cc_start: 0.7565 (m110) cc_final: 0.6830 (m110) REVERT: H 122 ILE cc_start: 0.8095 (tp) cc_final: 0.7845 (mm) REVERT: H 140 LEU cc_start: 0.8736 (mt) cc_final: 0.8475 (mp) REVERT: H 236 LEU cc_start: 0.7814 (pt) cc_final: 0.7359 (mt) REVERT: H 249 THR cc_start: 0.8043 (m) cc_final: 0.7550 (p) REVERT: H 294 TYR cc_start: 0.6928 (m-80) cc_final: 0.6516 (m-10) REVERT: H 299 MET cc_start: 0.6421 (mtp) cc_final: 0.6119 (mtp) REVERT: H 313 MET cc_start: 0.8173 (tpt) cc_final: 0.7822 (tpp) REVERT: H 329 ILE cc_start: 0.8185 (mm) cc_final: 0.7723 (mt) REVERT: H 352 PHE cc_start: 0.7740 (t80) cc_final: 0.6857 (t80) REVERT: H 356 TRP cc_start: 0.7726 (m100) cc_final: 0.6806 (m100) REVERT: I 82 MET cc_start: 0.8361 (mmt) cc_final: 0.7942 (mmm) REVERT: I 222 ASP cc_start: 0.6059 (p0) cc_final: 0.5385 (p0) REVERT: I 227 MET cc_start: 0.7976 (ttt) cc_final: 0.7594 (mtp) REVERT: I 241 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7124 (tm-30) REVERT: I 263 GLN cc_start: 0.8301 (mt0) cc_final: 0.7885 (tt0) REVERT: I 280 ASN cc_start: 0.7354 (m-40) cc_final: 0.7052 (m110) REVERT: I 314 GLN cc_start: 0.6928 (tp40) cc_final: 0.6453 (tp40) REVERT: I 316 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7416 (mm-30) REVERT: I 325 MET cc_start: 0.6681 (ppp) cc_final: 0.5935 (ppp) outliers start: 90 outliers final: 47 residues processed: 716 average time/residue: 0.2053 time to fit residues: 239.7263 Evaluate side-chains 620 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 571 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 ASN 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 101 THR Chi-restraints excluded: chain G residue 148 SER 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 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 30 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 83 GLU 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: 6.9990 chunk 51 optimal weight: 0.9990 chunk 160 optimal weight: 0.0370 chunk 345 optimal weight: 2.9990 chunk 408 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 384 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 286 HIS D 73 GLN D 150 GLN D 296 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 59 GLN H 121 GLN H 173 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091851 restraints weight = 86498.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094125 restraints weight = 43954.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095597 restraints weight = 27426.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096555 restraints weight = 19868.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097179 restraints weight = 16064.441| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 40029 Z= 0.137 Angle : 0.626 12.767 54328 Z= 0.309 Chirality : 0.045 0.187 6016 Planarity : 0.004 0.046 6988 Dihedral : 8.562 171.950 5545 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.54 % Allowed : 17.84 % Favored : 79.62 % 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 aren not related in a simple way. whole: 0.04 (0.12), residues: 4875 helix: 0.96 (0.12), residues: 1839 sheet: -0.58 (0.17), residues: 929 loop : -0.40 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 210 TYR 0.021 0.001 TYR A 246 PHE 0.023 0.001 PHE B 24 TRP 0.021 0.002 TRP Q 340 HIS 0.005 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00320 (40028) covalent geometry : angle 0.62579 (54326) SS BOND : bond 0.01100 ( 1) SS BOND : angle 1.75238 ( 2) hydrogen bonds : bond 0.03817 ( 1733) hydrogen bonds : angle 4.99785 ( 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 727 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 620 time to evaluate : 1.192 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: 0.4878 (OUTLIER) cc_final: 0.3497 (m-80) REVERT: A 95 ARG cc_start: 0.7409 (ptp-170) cc_final: 0.7004 (ptp-170) REVERT: A 133 LEU cc_start: 0.7339 (mp) cc_final: 0.6999 (tp) REVERT: A 214 ARG cc_start: 0.7017 (ttm170) cc_final: 0.6685 (ttm170) REVERT: A 231 ASP cc_start: 0.7410 (t0) cc_final: 0.7176 (t0) REVERT: A 281 ASP cc_start: 0.8017 (t0) cc_final: 0.7607 (t0) REVERT: A 295 ASN cc_start: 0.8319 (t0) cc_final: 0.7915 (t0) REVERT: A 368 LYS cc_start: 0.7802 (pptt) cc_final: 0.6695 (mmtm) REVERT: A 382 GLN cc_start: 0.8402 (mm110) cc_final: 0.8106 (tp-100) REVERT: B 19 TYR cc_start: 0.7601 (m-80) cc_final: 0.7079 (m-10) REVERT: B 39 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6959 (mtm180) REVERT: B 81 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 85 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 107 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: B 133 TYR cc_start: 0.8006 (t80) cc_final: 0.6808 (t80) REVERT: B 227 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7142 (t-90) REVERT: B 283 GLN cc_start: 0.7764 (tp40) cc_final: 0.7286 (mm110) REVERT: B 320 LEU cc_start: 0.8199 (tp) cc_final: 0.7857 (tp) REVERT: B 324 ARG cc_start: 0.7004 (tpp80) cc_final: 0.6769 (tpp80) REVERT: B 329 ASP cc_start: 0.7677 (t0) cc_final: 0.7293 (m-30) REVERT: C 69 ARG cc_start: 0.6472 (mtt90) cc_final: 0.6246 (mtt90) REVERT: C 258 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6698 (tp) REVERT: C 286 HIS cc_start: 0.7501 (t-90) cc_final: 0.7097 (t70) REVERT: D 109 MET cc_start: 0.8672 (tpp) cc_final: 0.8336 (tpp) REVERT: D 113 MET cc_start: 0.8038 (tpp) cc_final: 0.7369 (mmt) REVERT: D 129 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7789 (mmtp) REVERT: D 280 MET cc_start: 0.8772 (mmt) cc_final: 0.8399 (mmt) REVERT: E 79 GLU cc_start: 0.5815 (tp30) cc_final: 0.4963 (tp30) REVERT: E 83 ARG cc_start: 0.5664 (tpp80) cc_final: 0.5196 (tpp80) REVERT: E 97 ASN cc_start: 0.7864 (m-40) cc_final: 0.7436 (m-40) REVERT: E 98 SER cc_start: 0.8316 (t) cc_final: 0.7695 (p) REVERT: E 159 LYS cc_start: 0.6902 (pttm) cc_final: 0.6240 (ttpp) REVERT: F 58 GLN cc_start: 0.8333 (mp-120) cc_final: 0.8125 (mp10) REVERT: F 137 GLU cc_start: 0.7445 (tp30) cc_final: 0.7025 (tp30) REVERT: G 27 GLU cc_start: 0.7783 (tt0) cc_final: 0.7479 (tt0) REVERT: G 82 ASP cc_start: 0.8272 (m-30) cc_final: 0.8012 (m-30) REVERT: G 97 LYS cc_start: 0.6589 (ptmm) cc_final: 0.6290 (ptpp) REVERT: G 98 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5465 (mp0) REVERT: G 151 ASP cc_start: 0.6694 (p0) cc_final: 0.6273 (p0) REVERT: M 122 ILE cc_start: 0.8126 (mt) cc_final: 0.7829 (mm) REVERT: M 123 MET cc_start: 0.7906 (tpt) cc_final: 0.7090 (ttm) REVERT: N 44 MET cc_start: 0.5170 (tpt) cc_final: 0.4444 (mtm) REVERT: N 113 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7456 (mmmt) REVERT: O 84 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8492 (ttmt) REVERT: O 206 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7819 (ttp80) REVERT: O 330 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8450 (mt) REVERT: O 337 TYR cc_start: 0.7913 (m-80) cc_final: 0.7558 (m-80) REVERT: P 47 MET cc_start: 0.6928 (pmm) cc_final: 0.6580 (pmm) REVERT: P 69 TYR cc_start: 0.8277 (m-80) cc_final: 0.8010 (m-80) REVERT: P 227 MET cc_start: 0.8838 (mmm) cc_final: 0.8218 (mmt) REVERT: Q 47 MET cc_start: 0.6645 (mmm) cc_final: 0.5736 (ptp) REVERT: Q 283 MET cc_start: 0.8496 (mmm) cc_final: 0.8154 (mmt) REVERT: H 123 MET cc_start: 0.7748 (ttm) cc_final: 0.7239 (ttm) REVERT: H 140 LEU cc_start: 0.8733 (mt) cc_final: 0.8485 (mp) REVERT: H 236 LEU cc_start: 0.7836 (pt) cc_final: 0.7492 (mt) REVERT: H 249 THR cc_start: 0.8105 (m) cc_final: 0.7640 (p) REVERT: H 294 TYR cc_start: 0.6904 (m-80) cc_final: 0.6335 (m-10) REVERT: H 313 MET cc_start: 0.8114 (tpt) cc_final: 0.7766 (tpp) REVERT: H 329 ILE cc_start: 0.8146 (mm) cc_final: 0.7752 (mt) REVERT: H 352 PHE cc_start: 0.7915 (t80) cc_final: 0.7580 (t80) REVERT: H 355 MET cc_start: 0.6968 (pmm) cc_final: 0.6494 (pmm) REVERT: H 356 TRP cc_start: 0.7540 (m100) cc_final: 0.6489 (m100) REVERT: I 82 MET cc_start: 0.8390 (mmt) cc_final: 0.7966 (mmm) REVERT: I 154 ASP cc_start: 0.8202 (t70) cc_final: 0.7219 (t0) REVERT: I 222 ASP cc_start: 0.5983 (p0) cc_final: 0.5085 (p0) REVERT: I 227 MET cc_start: 0.7938 (ttt) cc_final: 0.7656 (mtp) REVERT: I 241 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7177 (tm-30) REVERT: I 263 GLN cc_start: 0.8408 (mt0) cc_final: 0.8031 (tt0) REVERT: I 280 ASN cc_start: 0.7335 (m-40) cc_final: 0.6989 (m110) REVERT: I 325 MET cc_start: 0.6538 (ppp) cc_final: 0.5791 (ppp) outliers start: 107 outliers final: 64 residues processed: 693 average time/residue: 0.2100 time to fit residues: 236.7048 Evaluate side-chains 647 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 577 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 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 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 160 HIS 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 59 ASN Chi-restraints excluded: chain E residue 93 GLU 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 61 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain N residue 103 THR 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 318 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 238 LYS Chi-restraints excluded: chain Q residue 330 ILE 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 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 83 GLU 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: 2.9990 chunk 221 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 481 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 259 optimal weight: 0.2980 chunk 190 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 73 GLN D 296 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN H 297 ASN I 49 GLN I 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089048 restraints weight = 87707.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091224 restraints weight = 44611.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092632 restraints weight = 28075.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093550 restraints weight = 20558.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094135 restraints weight = 16738.791| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 40029 Z= 0.256 Angle : 0.717 12.406 54328 Z= 0.360 Chirality : 0.049 0.188 6016 Planarity : 0.005 0.061 6988 Dihedral : 8.544 166.506 5545 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.32 % Allowed : 18.55 % Favored : 78.13 % 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 aren not related in a simple way. whole: -0.24 (0.12), residues: 4875 helix: 0.72 (0.12), residues: 1837 sheet: -0.75 (0.17), residues: 964 loop : -0.53 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 138 TYR 0.033 0.002 TYR D 65 PHE 0.019 0.002 PHE Q 127 TRP 0.026 0.002 TRP M 340 HIS 0.007 0.001 HIS P 87 Details of bonding type rmsd covalent geometry : bond 0.00608 (40028) covalent geometry : angle 0.71691 (54326) SS BOND : bond 0.01084 ( 1) SS BOND : angle 2.25157 ( 2) hydrogen bonds : bond 0.04543 ( 1733) hydrogen bonds : angle 5.15496 ( 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 716 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 576 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5368 (OUTLIER) cc_final: 0.3856 (m-80) REVERT: A 133 LEU cc_start: 0.7481 (mp) cc_final: 0.7183 (tp) REVERT: A 231 ASP cc_start: 0.7346 (t0) cc_final: 0.7036 (t0) REVERT: A 281 ASP cc_start: 0.8036 (t0) cc_final: 0.7725 (t0) REVERT: B 19 TYR cc_start: 0.7641 (m-80) cc_final: 0.7095 (m-10) REVERT: B 81 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7470 (mt-10) REVERT: B 85 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 107 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: B 133 TYR cc_start: 0.8139 (t80) cc_final: 0.7032 (t80) REVERT: B 227 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7326 (t-90) REVERT: B 277 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7424 (t80) REVERT: B 283 GLN cc_start: 0.7922 (tp40) cc_final: 0.7437 (mm110) REVERT: B 320 LEU cc_start: 0.8270 (tp) cc_final: 0.7958 (tp) REVERT: B 324 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6617 (tpp80) REVERT: B 329 ASP cc_start: 0.7690 (t0) cc_final: 0.7445 (m-30) REVERT: B 361 MET cc_start: 0.7894 (ttp) cc_final: 0.7624 (ttp) REVERT: C 69 ARG cc_start: 0.6510 (mtt90) cc_final: 0.6301 (mtt90) REVERT: C 131 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6797 (tm-30) REVERT: D 129 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7861 (mmtp) REVERT: D 205 ARG cc_start: 0.7398 (mtm180) cc_final: 0.7175 (mtm110) REVERT: E 61 GLU cc_start: 0.5661 (tp30) cc_final: 0.5373 (tp30) REVERT: E 97 ASN cc_start: 0.7857 (m-40) cc_final: 0.7462 (m-40) REVERT: E 98 SER cc_start: 0.8591 (t) cc_final: 0.7874 (p) REVERT: F 119 THR cc_start: 0.9326 (m) cc_final: 0.9115 (p) REVERT: F 137 GLU cc_start: 0.7601 (tp30) cc_final: 0.7108 (tp30) REVERT: G 82 ASP cc_start: 0.8226 (m-30) cc_final: 0.7963 (m-30) REVERT: G 87 ILE cc_start: 0.7165 (mt) cc_final: 0.6886 (mt) REVERT: G 151 ASP cc_start: 0.6729 (p0) cc_final: 0.6364 (p0) REVERT: M 122 ILE cc_start: 0.8408 (mt) cc_final: 0.8167 (mm) REVERT: M 289 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8873 (pt) REVERT: N 44 MET cc_start: 0.5358 (tpt) cc_final: 0.4521 (mtm) REVERT: O 206 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7822 (ttp80) REVERT: O 330 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8421 (mt) REVERT: O 337 TYR cc_start: 0.8004 (m-80) cc_final: 0.7665 (m-80) REVERT: P 69 TYR cc_start: 0.8147 (m-80) cc_final: 0.7857 (m-80) REVERT: P 227 MET cc_start: 0.8818 (mmm) cc_final: 0.8538 (mmt) REVERT: Q 47 MET cc_start: 0.6605 (mmm) cc_final: 0.5734 (ptp) REVERT: Q 283 MET cc_start: 0.8494 (mmm) cc_final: 0.7973 (mmp) REVERT: R 94 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7769 (mp) REVERT: R 269 MET cc_start: 0.8186 (ttm) cc_final: 0.7717 (ttm) REVERT: H 140 LEU cc_start: 0.8821 (mt) cc_final: 0.8602 (mp) REVERT: H 236 LEU cc_start: 0.7765 (pt) cc_final: 0.7274 (mt) REVERT: H 249 THR cc_start: 0.8219 (m) cc_final: 0.7764 (p) REVERT: H 294 TYR cc_start: 0.7043 (m-80) cc_final: 0.6243 (m-10) REVERT: H 305 MET cc_start: 0.6063 (tpt) cc_final: 0.5724 (tpt) REVERT: H 313 MET cc_start: 0.8170 (tpt) cc_final: 0.7769 (tpp) REVERT: H 325 MET cc_start: 0.7406 (mmt) cc_final: 0.7085 (mmt) REVERT: H 352 PHE cc_start: 0.8011 (t80) cc_final: 0.7614 (t80) REVERT: H 355 MET cc_start: 0.6719 (pmm) cc_final: 0.6261 (pmm) REVERT: H 356 TRP cc_start: 0.7370 (m100) cc_final: 0.6520 (m100) REVERT: I 50 LYS cc_start: 0.8095 (mmpt) cc_final: 0.7728 (mmmt) REVERT: I 59 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7527 (tp-100) REVERT: I 82 MET cc_start: 0.8373 (mmt) cc_final: 0.7952 (mmm) REVERT: I 154 ASP cc_start: 0.8205 (t70) cc_final: 0.7262 (t70) REVERT: I 178 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7616 (tt) REVERT: I 207 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7452 (mm-30) REVERT: I 222 ASP cc_start: 0.6373 (p0) cc_final: 0.5518 (p0) REVERT: I 280 ASN cc_start: 0.7372 (m-40) cc_final: 0.7021 (m110) REVERT: I 314 GLN cc_start: 0.6277 (tp40) cc_final: 0.5979 (tp40) REVERT: I 325 MET cc_start: 0.6457 (ppp) cc_final: 0.5705 (ppp) outliers start: 140 outliers final: 99 residues processed: 683 average time/residue: 0.2076 time to fit residues: 231.0803 Evaluate side-chains 642 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 534 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 85 LEU 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 96 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 160 HIS 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 59 ASN 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 G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 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 92 ASN Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 267 ILE 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 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU 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 253 GLU Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 10 CYS 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 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 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 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 30 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 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 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 241 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 383 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 479 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 83 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS H 297 ASN I 49 GLN I 162 ASN I 263 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090526 restraints weight = 87765.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092742 restraints weight = 44234.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093360 restraints weight = 25538.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093558 restraints weight = 23072.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093589 restraints weight = 20862.993| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 40029 Z= 0.209 Angle : 0.683 12.149 54328 Z= 0.340 Chirality : 0.047 0.236 6016 Planarity : 0.005 0.065 6988 Dihedral : 8.362 163.113 5545 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.37 % Allowed : 19.36 % Favored : 77.27 % 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 aren not related in a simple way. whole: -0.24 (0.12), residues: 4875 helix: 0.69 (0.12), residues: 1845 sheet: -0.69 (0.17), residues: 949 loop : -0.54 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 167 TYR 0.036 0.002 TYR D 65 PHE 0.017 0.002 PHE D 250 TRP 0.057 0.002 TRP G 129 HIS 0.008 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00496 (40028) covalent geometry : angle 0.68250 (54326) SS BOND : bond 0.01105 ( 1) SS BOND : angle 2.25994 ( 2) hydrogen bonds : bond 0.04238 ( 1733) hydrogen bonds : angle 5.07808 ( 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 706 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 564 time to evaluate : 1.301 Fit side-chains 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: 0.3923 (m-80) REVERT: A 148 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 214 ARG cc_start: 0.7090 (ttm170) cc_final: 0.6837 (ttm170) REVERT: A 264 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6567 (mpt180) REVERT: A 281 ASP cc_start: 0.8027 (t0) cc_final: 0.7687 (t0) REVERT: B 19 TYR cc_start: 0.7612 (m-80) cc_final: 0.7211 (m-10) REVERT: B 81 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7396 (mt-10) REVERT: B 85 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 107 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: B 133 TYR cc_start: 0.8173 (t80) cc_final: 0.7078 (t80) REVERT: B 227 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7320 (t-90) REVERT: B 277 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7449 (t80) REVERT: B 283 GLN cc_start: 0.7919 (tp40) cc_final: 0.7476 (mm110) REVERT: B 320 LEU cc_start: 0.8263 (tp) cc_final: 0.7903 (tp) REVERT: B 324 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6536 (tpp80) REVERT: B 361 MET cc_start: 0.7686 (ttp) cc_final: 0.7307 (ttp) REVERT: C 131 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6899 (tm-30) REVERT: D 129 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7875 (mmtp) REVERT: D 205 ARG cc_start: 0.7274 (mtm180) cc_final: 0.7059 (mtm110) REVERT: D 280 MET cc_start: 0.8789 (mmt) cc_final: 0.8370 (mmp) REVERT: E 97 ASN cc_start: 0.7862 (m-40) cc_final: 0.7476 (m-40) REVERT: E 98 SER cc_start: 0.8483 (t) cc_final: 0.7846 (p) REVERT: E 159 LYS cc_start: 0.6963 (pttm) cc_final: 0.6652 (ttpp) REVERT: F 137 GLU cc_start: 0.7557 (tp30) cc_final: 0.7112 (tp30) REVERT: G 82 ASP cc_start: 0.8271 (m-30) cc_final: 0.7992 (m-30) REVERT: G 98 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5459 (mp0) REVERT: M 122 ILE cc_start: 0.8389 (mt) cc_final: 0.8140 (mm) REVERT: M 123 MET cc_start: 0.7735 (tpp) cc_final: 0.7141 (ttm) REVERT: M 289 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8857 (pt) REVERT: N 44 MET cc_start: 0.5350 (tpt) cc_final: 0.4422 (mtm) REVERT: N 94 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8593 (mm) REVERT: O 147 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7651 (mtt-85) REVERT: O 206 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7706 (ttp80) REVERT: O 330 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8285 (mt) REVERT: O 337 TYR cc_start: 0.7979 (m-80) cc_final: 0.7662 (m-80) REVERT: P 68 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8217 (mtpp) REVERT: P 69 TYR cc_start: 0.8157 (m-80) cc_final: 0.7899 (m-80) REVERT: P 227 MET cc_start: 0.8777 (mmm) cc_final: 0.8527 (mmt) REVERT: Q 47 MET cc_start: 0.6903 (mmm) cc_final: 0.5913 (ptp) REVERT: Q 283 MET cc_start: 0.8472 (mmm) cc_final: 0.7968 (mmp) REVERT: R 269 MET cc_start: 0.8139 (ttm) cc_final: 0.7701 (ttm) REVERT: H 47 MET cc_start: 0.7548 (pmm) cc_final: 0.7327 (pmm) REVERT: H 140 LEU cc_start: 0.8744 (mt) cc_final: 0.8504 (mp) REVERT: H 236 LEU cc_start: 0.7805 (pt) cc_final: 0.7273 (mt) REVERT: H 249 THR cc_start: 0.8172 (m) cc_final: 0.7786 (p) REVERT: H 294 TYR cc_start: 0.7120 (m-80) cc_final: 0.6266 (m-10) REVERT: H 352 PHE cc_start: 0.7838 (t80) cc_final: 0.7490 (t80) REVERT: H 355 MET cc_start: 0.6922 (pmm) cc_final: 0.6534 (pmm) REVERT: H 356 TRP cc_start: 0.7437 (m100) cc_final: 0.6502 (m100) REVERT: I 45 VAL cc_start: 0.6576 (OUTLIER) cc_final: 0.6371 (t) REVERT: I 50 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7720 (mmmt) REVERT: I 59 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7516 (tp-100) REVERT: I 82 MET cc_start: 0.8356 (mmt) cc_final: 0.7940 (mmm) REVERT: I 154 ASP cc_start: 0.8136 (t70) cc_final: 0.7249 (t70) REVERT: I 178 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7599 (tt) REVERT: I 207 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7434 (mm-30) REVERT: I 222 ASP cc_start: 0.6259 (p0) cc_final: 0.5400 (p0) REVERT: I 263 GLN cc_start: 0.8045 (mt0) cc_final: 0.7670 (mt0) REVERT: I 280 ASN cc_start: 0.7338 (m-40) cc_final: 0.7015 (m110) REVERT: I 314 GLN cc_start: 0.6384 (tp40) cc_final: 0.6051 (tp40) REVERT: I 325 MET cc_start: 0.6487 (ppp) cc_final: 0.5793 (ppp) outliers start: 142 outliers final: 102 residues processed: 670 average time/residue: 0.1987 time to fit residues: 218.2801 Evaluate side-chains 649 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 535 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 85 LEU Chi-restraints excluded: chain B residue 107 GLU 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 181 ASP 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 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 160 HIS 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 91 ASP 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 63 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 41 GLN Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 94 LEU 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 159 VAL 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 O residue 330 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 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 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 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 30 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 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 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: 0.0980 chunk 305 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 473 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN D 73 GLN D 296 ASN O 49 GLN O 275 HIS R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN H 173 HIS H 297 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091270 restraints weight = 85942.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093543 restraints weight = 43499.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095014 restraints weight = 27164.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095982 restraints weight = 19701.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096516 restraints weight = 15885.585| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40029 Z= 0.121 Angle : 0.631 11.803 54328 Z= 0.310 Chirality : 0.045 0.193 6016 Planarity : 0.004 0.055 6988 Dihedral : 7.938 162.653 5545 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.63 % Allowed : 20.14 % Favored : 77.22 % 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 aren not related in a simple way. whole: 0.06 (0.12), residues: 4875 helix: 0.95 (0.12), residues: 1841 sheet: -0.54 (0.17), residues: 948 loop : -0.36 (0.15), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 167 TYR 0.023 0.001 TYR A 265 PHE 0.017 0.001 PHE D 250 TRP 0.031 0.002 TRP G 129 HIS 0.007 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00273 (40028) covalent geometry : angle 0.63047 (54326) SS BOND : bond 0.01485 ( 1) SS BOND : angle 2.16489 ( 2) hydrogen bonds : bond 0.03613 ( 1733) hydrogen bonds : angle 4.89436 ( 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 697 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 586 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5258 (OUTLIER) cc_final: 0.3801 (m-80) REVERT: A 148 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 214 ARG cc_start: 0.7052 (ttm170) cc_final: 0.6788 (ttm170) REVERT: A 264 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6593 (mpt180) REVERT: B 19 TYR cc_start: 0.7566 (m-80) cc_final: 0.7033 (m-10) REVERT: B 81 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7390 (mt-10) REVERT: B 82 MET cc_start: 0.8110 (tpt) cc_final: 0.7809 (tpt) REVERT: B 85 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8741 (tt) REVERT: B 107 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: B 133 TYR cc_start: 0.8243 (t80) cc_final: 0.7199 (t80) REVERT: B 227 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7237 (t-90) REVERT: B 277 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 320 LEU cc_start: 0.8197 (tp) cc_final: 0.7818 (tp) REVERT: B 324 ARG cc_start: 0.7023 (tpp80) cc_final: 0.6759 (tpp80) REVERT: C 91 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7568 (pttm) REVERT: D 113 MET cc_start: 0.7935 (tpp) cc_final: 0.7384 (mmt) REVERT: E 97 ASN cc_start: 0.7863 (m-40) cc_final: 0.7475 (m-40) REVERT: E 98 SER cc_start: 0.8491 (t) cc_final: 0.7843 (p) REVERT: G 82 ASP cc_start: 0.8277 (m-30) cc_final: 0.8002 (m-30) REVERT: G 98 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5582 (mp0) REVERT: M 122 ILE cc_start: 0.8421 (mt) cc_final: 0.8177 (mm) REVERT: M 123 MET cc_start: 0.7583 (tpp) cc_final: 0.7103 (ttm) REVERT: N 41 GLN cc_start: 0.4691 (pm20) cc_final: 0.4424 (pm20) REVERT: N 44 MET cc_start: 0.5247 (tpt) cc_final: 0.4417 (mtm) REVERT: N 123 MET cc_start: 0.8083 (ttm) cc_final: 0.7576 (mtp) REVERT: O 206 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7793 (ttp80) REVERT: O 283 MET cc_start: 0.9003 (mmm) cc_final: 0.8779 (mmp) REVERT: O 330 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8280 (mt) REVERT: O 337 TYR cc_start: 0.7863 (m-80) cc_final: 0.7510 (m-80) REVERT: O 353 GLN cc_start: 0.8410 (mp10) cc_final: 0.8111 (mp10) REVERT: P 69 TYR cc_start: 0.8196 (m-80) cc_final: 0.7967 (m-80) REVERT: P 180 LEU cc_start: 0.9056 (tp) cc_final: 0.8842 (tp) REVERT: P 227 MET cc_start: 0.8791 (mmm) cc_final: 0.8140 (mmt) REVERT: Q 47 MET cc_start: 0.6744 (mmm) cc_final: 0.5821 (ptp) REVERT: Q 176 MET cc_start: 0.7818 (mmm) cc_final: 0.7580 (mmt) REVERT: Q 283 MET cc_start: 0.8520 (mmm) cc_final: 0.8160 (mmt) REVERT: R 205 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6722 (mp0) REVERT: R 269 MET cc_start: 0.8129 (ttm) cc_final: 0.7756 (ttm) REVERT: H 140 LEU cc_start: 0.8675 (mt) cc_final: 0.8386 (mp) REVERT: H 236 LEU cc_start: 0.7627 (pt) cc_final: 0.7369 (mt) REVERT: H 249 THR cc_start: 0.8142 (m) cc_final: 0.7715 (p) REVERT: H 290 ARG cc_start: 0.7594 (ptp-110) cc_final: 0.7258 (ptp-110) REVERT: H 294 TYR cc_start: 0.7105 (m-80) cc_final: 0.6337 (m-10) REVERT: H 313 MET cc_start: 0.8051 (tpt) cc_final: 0.7762 (tpp) REVERT: H 352 PHE cc_start: 0.7717 (t80) cc_final: 0.7361 (t80) REVERT: H 355 MET cc_start: 0.7103 (pmm) cc_final: 0.6671 (pmm) REVERT: H 356 TRP cc_start: 0.7456 (m100) cc_final: 0.6536 (m100) REVERT: I 50 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7732 (mmmt) REVERT: I 59 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7443 (tp40) REVERT: I 82 MET cc_start: 0.8408 (mmt) cc_final: 0.7987 (mmm) REVERT: I 154 ASP cc_start: 0.8198 (t70) cc_final: 0.7249 (t70) REVERT: I 207 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7411 (mm-30) REVERT: I 222 ASP cc_start: 0.6241 (p0) cc_final: 0.5418 (p0) REVERT: I 241 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7227 (tm-30) REVERT: I 244 ASP cc_start: 0.7321 (p0) cc_final: 0.7021 (p0) REVERT: I 280 ASN cc_start: 0.7286 (m-40) cc_final: 0.6919 (m110) REVERT: I 314 GLN cc_start: 0.6488 (tp40) cc_final: 0.6223 (tp40) REVERT: I 316 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7419 (mm-30) REVERT: I 325 MET cc_start: 0.6231 (ppp) cc_final: 0.5694 (ppp) outliers start: 111 outliers final: 79 residues processed: 669 average time/residue: 0.2109 time to fit residues: 230.0077 Evaluate side-chains 635 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 549 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 264 ARG 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 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 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 160 HIS 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 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 63 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 41 GLN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 159 VAL 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 137 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 422 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 403 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 316 GLN B 10 ASN B 48 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 263 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091416 restraints weight = 86279.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093676 restraints weight = 43767.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095163 restraints weight = 27342.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096109 restraints weight = 19800.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096732 restraints weight = 16003.398| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40029 Z= 0.123 Angle : 0.636 15.819 54328 Z= 0.311 Chirality : 0.045 0.201 6016 Planarity : 0.004 0.058 6988 Dihedral : 7.785 161.162 5545 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.78 % Allowed : 20.62 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.13), residues: 4875 helix: 0.99 (0.12), residues: 1841 sheet: -0.47 (0.17), residues: 946 loop : -0.29 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 167 TYR 0.029 0.001 TYR G 112 PHE 0.018 0.001 PHE D 250 TRP 0.029 0.002 TRP E 160 HIS 0.005 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00284 (40028) covalent geometry : angle 0.63589 (54326) SS BOND : bond 0.00581 ( 1) SS BOND : angle 2.26764 ( 2) hydrogen bonds : bond 0.03562 ( 1733) hydrogen bonds : angle 4.83377 ( 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 692 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 575 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5292 (OUTLIER) cc_final: 0.3883 (m-80) REVERT: A 101 ASN cc_start: 0.6362 (t0) cc_final: 0.6042 (t0) REVERT: A 148 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 214 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6853 (ttm170) REVERT: A 264 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6673 (mpt180) REVERT: B 19 TYR cc_start: 0.7548 (m-80) cc_final: 0.7043 (m-10) REVERT: B 81 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 85 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 107 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 133 TYR cc_start: 0.8091 (t80) cc_final: 0.7372 (t80) REVERT: B 227 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7198 (t-90) REVERT: B 277 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7352 (t80) REVERT: B 283 GLN cc_start: 0.7799 (tp40) cc_final: 0.7328 (mm110) REVERT: B 320 LEU cc_start: 0.8220 (tp) cc_final: 0.7859 (tp) REVERT: B 324 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6751 (tpp80) REVERT: C 286 HIS cc_start: 0.7798 (t70) cc_final: 0.7510 (t-90) REVERT: D 113 MET cc_start: 0.7995 (tpp) cc_final: 0.7472 (mmt) REVERT: D 287 ARG cc_start: 0.6779 (ttm170) cc_final: 0.6566 (ttm170) REVERT: E 97 ASN cc_start: 0.7834 (m-40) cc_final: 0.7436 (m-40) REVERT: E 98 SER cc_start: 0.8488 (t) cc_final: 0.7852 (p) REVERT: G 82 ASP cc_start: 0.8267 (m-30) cc_final: 0.7995 (m-30) REVERT: G 98 GLU cc_start: 0.5842 (mm-30) cc_final: 0.5343 (mp0) REVERT: M 122 ILE cc_start: 0.8439 (mt) cc_final: 0.8174 (mm) REVERT: M 123 MET cc_start: 0.7585 (tpp) cc_final: 0.7302 (ttm) REVERT: N 44 MET cc_start: 0.5325 (tpt) cc_final: 0.4498 (mtm) REVERT: N 94 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (mm) REVERT: N 123 MET cc_start: 0.8085 (ttm) cc_final: 0.7577 (mtp) REVERT: O 44 MET cc_start: 0.7570 (tpt) cc_final: 0.7366 (tpt) REVERT: O 206 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7807 (ttp80) REVERT: O 330 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8395 (mt) REVERT: O 337 TYR cc_start: 0.7790 (m-80) cc_final: 0.7400 (m-80) REVERT: O 353 GLN cc_start: 0.8392 (mp10) cc_final: 0.8102 (mp10) REVERT: P 68 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: P 69 TYR cc_start: 0.8199 (m-80) cc_final: 0.7962 (m-80) REVERT: P 180 LEU cc_start: 0.9031 (tp) cc_final: 0.8825 (tp) REVERT: P 227 MET cc_start: 0.8782 (mmm) cc_final: 0.8140 (mmt) REVERT: P 325 MET cc_start: 0.7722 (ptp) cc_final: 0.7386 (ptp) REVERT: Q 47 MET cc_start: 0.6763 (mmm) cc_final: 0.5729 (ptp) REVERT: Q 176 MET cc_start: 0.7783 (mmm) cc_final: 0.7554 (mmt) REVERT: Q 283 MET cc_start: 0.8510 (mmm) cc_final: 0.8159 (mmt) REVERT: R 269 MET cc_start: 0.8125 (ttm) cc_final: 0.7762 (ttm) REVERT: H 140 LEU cc_start: 0.8652 (mt) cc_final: 0.8359 (mp) REVERT: H 236 LEU cc_start: 0.7629 (pt) cc_final: 0.7377 (mt) REVERT: H 249 THR cc_start: 0.8177 (m) cc_final: 0.7725 (p) REVERT: H 294 TYR cc_start: 0.7081 (m-80) cc_final: 0.6782 (m-80) REVERT: H 352 PHE cc_start: 0.7678 (t80) cc_final: 0.7310 (t80) REVERT: H 355 MET cc_start: 0.7103 (pmm) cc_final: 0.6680 (pmm) REVERT: H 356 TRP cc_start: 0.7368 (m100) cc_final: 0.6520 (m100) REVERT: I 45 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.6249 (t) REVERT: I 50 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7724 (mmmt) REVERT: I 82 MET cc_start: 0.8412 (mmt) cc_final: 0.7962 (mmm) REVERT: I 207 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7579 (mm-30) REVERT: I 222 ASP cc_start: 0.6388 (p0) cc_final: 0.5649 (p0) REVERT: I 241 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7294 (tm-30) REVERT: I 244 ASP cc_start: 0.7294 (p0) cc_final: 0.7009 (p0) REVERT: I 263 GLN cc_start: 0.8087 (mt0) cc_final: 0.7832 (mt0) REVERT: I 280 ASN cc_start: 0.7274 (m-40) cc_final: 0.6920 (m110) REVERT: I 314 GLN cc_start: 0.6544 (tp40) cc_final: 0.6273 (tp40) REVERT: I 316 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7421 (mm-30) REVERT: I 325 MET cc_start: 0.6091 (ppp) cc_final: 0.5572 (ppp) outliers start: 117 outliers final: 88 residues processed: 663 average time/residue: 0.2048 time to fit residues: 221.9022 Evaluate side-chains 650 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 552 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 316 GLN 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 D residue 100 THR Chi-restraints excluded: chain D residue 160 HIS 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 63 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 41 GLN 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 202 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 165 ILE 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 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 159 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 330 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 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 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 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 115 ASN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 246 GLN 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 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: 0.2980 chunk 374 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 283 optimal weight: 0.1980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 352 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN I 173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090310 restraints weight = 86838.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092562 restraints weight = 43881.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094025 restraints weight = 27350.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094968 restraints weight = 19828.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095581 restraints weight = 16012.895| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 40029 Z= 0.166 Angle : 0.663 15.798 54328 Z= 0.325 Chirality : 0.046 0.229 6016 Planarity : 0.005 0.058 6988 Dihedral : 7.795 157.673 5545 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.85 % Allowed : 20.83 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.12), residues: 4875 helix: 0.95 (0.12), residues: 1838 sheet: -0.50 (0.17), residues: 944 loop : -0.33 (0.15), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 167 TYR 0.033 0.001 TYR G 112 PHE 0.019 0.001 PHE D 250 TRP 0.026 0.002 TRP G 129 HIS 0.005 0.001 HIS I 173 Details of bonding type rmsd covalent geometry : bond 0.00394 (40028) covalent geometry : angle 0.66266 (54326) SS BOND : bond 0.00742 ( 1) SS BOND : angle 2.32932 ( 2) hydrogen bonds : bond 0.03782 ( 1733) hydrogen bonds : angle 4.86680 ( 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 678 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 558 time to evaluate : 1.213 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: 0.5395 (OUTLIER) cc_final: 0.3952 (m-80) REVERT: A 264 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6638 (mpt180) REVERT: B 19 TYR cc_start: 0.7549 (m-80) cc_final: 0.7074 (m-10) REVERT: B 85 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 107 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 227 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7224 (t-90) REVERT: B 277 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7378 (t80) REVERT: B 283 GLN cc_start: 0.7830 (tp40) cc_final: 0.7317 (mm110) REVERT: B 320 LEU cc_start: 0.8358 (tp) cc_final: 0.8020 (tp) REVERT: B 324 ARG cc_start: 0.7015 (tpp80) cc_final: 0.6735 (tpp80) REVERT: C 286 HIS cc_start: 0.7896 (t70) cc_final: 0.7349 (t70) REVERT: D 287 ARG cc_start: 0.7033 (ttm170) cc_final: 0.6774 (ttm170) REVERT: E 97 ASN cc_start: 0.7827 (m-40) cc_final: 0.7436 (m-40) REVERT: E 98 SER cc_start: 0.8493 (t) cc_final: 0.7878 (p) REVERT: E 154 LYS cc_start: 0.6621 (tptp) cc_final: 0.6347 (tptt) REVERT: F 137 GLU cc_start: 0.7513 (tp30) cc_final: 0.7057 (tp30) REVERT: G 82 ASP cc_start: 0.8265 (m-30) cc_final: 0.7986 (m-30) REVERT: G 98 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5392 (mp0) REVERT: M 122 ILE cc_start: 0.8488 (mt) cc_final: 0.8233 (mm) REVERT: M 123 MET cc_start: 0.7676 (tpp) cc_final: 0.7110 (ttm) REVERT: N 44 MET cc_start: 0.5304 (tpt) cc_final: 0.4603 (mtm) REVERT: N 94 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8607 (mm) REVERT: O 206 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7822 (ttp80) REVERT: O 330 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8466 (mt) REVERT: O 337 TYR cc_start: 0.7843 (m-80) cc_final: 0.7446 (m-80) REVERT: P 68 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: P 69 TYR cc_start: 0.8213 (m-80) cc_final: 0.7957 (m-80) REVERT: P 180 LEU cc_start: 0.9110 (tp) cc_final: 0.8862 (tp) REVERT: P 227 MET cc_start: 0.8795 (mmm) cc_final: 0.8129 (mmt) REVERT: P 325 MET cc_start: 0.7805 (ptp) cc_final: 0.7490 (ptp) REVERT: Q 47 MET cc_start: 0.6822 (mmm) cc_final: 0.5708 (ptp) REVERT: Q 283 MET cc_start: 0.8516 (mmm) cc_final: 0.8129 (mmt) REVERT: R 269 MET cc_start: 0.8164 (ttm) cc_final: 0.7831 (ttm) REVERT: H 12 ASN cc_start: 0.8184 (m-40) cc_final: 0.7876 (m-40) REVERT: H 140 LEU cc_start: 0.8645 (mt) cc_final: 0.8341 (mp) REVERT: H 249 THR cc_start: 0.8134 (m) cc_final: 0.7746 (p) REVERT: H 260 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7944 (p) REVERT: H 294 TYR cc_start: 0.7025 (m-80) cc_final: 0.6800 (m-80) REVERT: H 352 PHE cc_start: 0.7604 (t80) cc_final: 0.7216 (t80) REVERT: H 355 MET cc_start: 0.7014 (pmm) cc_final: 0.6708 (pmm) REVERT: H 356 TRP cc_start: 0.7370 (m100) cc_final: 0.6558 (m100) REVERT: I 50 LYS cc_start: 0.8039 (mmpt) cc_final: 0.7673 (mmmt) REVERT: I 82 MET cc_start: 0.8398 (mmt) cc_final: 0.7955 (mmm) REVERT: I 154 ASP cc_start: 0.8211 (t70) cc_final: 0.7432 (t70) REVERT: I 207 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7600 (mm-30) REVERT: I 222 ASP cc_start: 0.6389 (p0) cc_final: 0.5651 (p0) REVERT: I 241 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7253 (tm-30) REVERT: I 244 ASP cc_start: 0.7313 (p0) cc_final: 0.7037 (p0) REVERT: I 263 GLN cc_start: 0.8166 (mt0) cc_final: 0.7845 (mt0) REVERT: I 280 ASN cc_start: 0.7275 (m-40) cc_final: 0.6915 (m110) REVERT: I 314 GLN cc_start: 0.6375 (tp40) cc_final: 0.6174 (tp40) REVERT: I 316 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7400 (mm-30) REVERT: I 325 MET cc_start: 0.6239 (ppp) cc_final: 0.5726 (ppp) outliers start: 120 outliers final: 95 residues processed: 646 average time/residue: 0.2114 time to fit residues: 222.5382 Evaluate side-chains 650 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 545 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 VAL 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 8 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 50 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 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 D residue 100 THR Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 291 PHE 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 63 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 41 GLN 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 202 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 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 159 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 330 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 R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 123 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 216 LEU Chi-restraints excluded: chain H residue 260 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 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 246 GLN 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: 0.0000 chunk 57 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 476 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 438 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 442 optimal weight: 0.7980 chunk 482 optimal weight: 5.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN M 101 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091801 restraints weight = 85758.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094072 restraints weight = 43573.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095551 restraints weight = 27199.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096501 restraints weight = 19718.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097076 restraints weight = 15954.951| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40029 Z= 0.122 Angle : 0.644 15.784 54328 Z= 0.315 Chirality : 0.045 0.220 6016 Planarity : 0.004 0.065 6988 Dihedral : 7.602 157.804 5545 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.40 % Allowed : 21.19 % Favored : 76.42 % 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 aren not related in a simple way. whole: 0.19 (0.13), residues: 4875 helix: 1.01 (0.12), residues: 1846 sheet: -0.47 (0.17), residues: 949 loop : -0.26 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 167 TYR 0.024 0.001 TYR I 218 PHE 0.020 0.001 PHE D 250 TRP 0.027 0.001 TRP G 129 HIS 0.005 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00281 (40028) covalent geometry : angle 0.64410 (54326) SS BOND : bond 0.00448 ( 1) SS BOND : angle 2.01048 ( 2) hydrogen bonds : bond 0.03479 ( 1733) hydrogen bonds : angle 4.79258 ( 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 665 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 564 time to evaluate : 1.086 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: 0.5344 (OUTLIER) cc_final: 0.3898 (m-80) REVERT: A 101 ASN cc_start: 0.6394 (t0) cc_final: 0.6128 (t0) REVERT: A 194 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 19 TYR cc_start: 0.7544 (m-80) cc_final: 0.7092 (m-10) REVERT: B 85 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8694 (tt) REVERT: B 107 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: B 227 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7238 (t-90) REVERT: B 277 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 283 GLN cc_start: 0.7737 (tp40) cc_final: 0.7248 (mm110) REVERT: B 320 LEU cc_start: 0.8339 (tp) cc_final: 0.7992 (tp) REVERT: B 324 ARG cc_start: 0.6942 (tpp80) cc_final: 0.6679 (tpp80) REVERT: C 286 HIS cc_start: 0.7868 (t70) cc_final: 0.7582 (t-90) REVERT: D 113 MET cc_start: 0.8141 (mmt) cc_final: 0.7590 (mmt) REVERT: D 125 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6766 (ttm170) REVERT: E 76 PHE cc_start: 0.6245 (t80) cc_final: 0.5890 (t80) REVERT: E 97 ASN cc_start: 0.7829 (m-40) cc_final: 0.7426 (m-40) REVERT: E 98 SER cc_start: 0.8395 (t) cc_final: 0.7787 (p) REVERT: G 82 ASP cc_start: 0.8253 (m-30) cc_final: 0.7961 (m-30) REVERT: G 98 GLU cc_start: 0.5834 (mm-30) cc_final: 0.5353 (mp0) REVERT: M 122 ILE cc_start: 0.8453 (mt) cc_final: 0.8179 (mm) REVERT: M 123 MET cc_start: 0.7573 (tpp) cc_final: 0.7060 (ttm) REVERT: N 44 MET cc_start: 0.5222 (tpt) cc_final: 0.4566 (mtm) REVERT: N 94 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8605 (mm) REVERT: N 123 MET cc_start: 0.8083 (ttm) cc_final: 0.7586 (mtp) REVERT: O 206 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7807 (ttp80) REVERT: O 330 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8362 (mt) REVERT: O 337 TYR cc_start: 0.7762 (m-80) cc_final: 0.7348 (m-80) REVERT: O 353 GLN cc_start: 0.8470 (mp10) cc_final: 0.8190 (mp10) REVERT: P 69 TYR cc_start: 0.8200 (m-80) cc_final: 0.7957 (m-80) REVERT: P 180 LEU cc_start: 0.9090 (tp) cc_final: 0.8824 (tp) REVERT: P 227 MET cc_start: 0.8768 (mmm) cc_final: 0.8119 (mmt) REVERT: Q 47 MET cc_start: 0.6726 (mmm) cc_final: 0.5637 (ptp) REVERT: Q 283 MET cc_start: 0.8507 (mmm) cc_final: 0.8152 (mmp) REVERT: R 269 MET cc_start: 0.8125 (ttm) cc_final: 0.7801 (ttm) REVERT: H 140 LEU cc_start: 0.8607 (mt) cc_final: 0.8309 (mp) REVERT: H 249 THR cc_start: 0.8154 (m) cc_final: 0.7740 (p) REVERT: H 294 TYR cc_start: 0.7014 (m-80) cc_final: 0.6789 (m-80) REVERT: H 313 MET cc_start: 0.8056 (tpt) cc_final: 0.7749 (tpp) REVERT: H 355 MET cc_start: 0.7144 (pmm) cc_final: 0.6883 (pmm) REVERT: I 50 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7644 (mmmt) REVERT: I 82 MET cc_start: 0.8398 (mmt) cc_final: 0.7965 (mmm) REVERT: I 154 ASP cc_start: 0.8197 (t70) cc_final: 0.7427 (t70) REVERT: I 207 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7621 (mm-30) REVERT: I 222 ASP cc_start: 0.6362 (p0) cc_final: 0.5630 (p0) REVERT: I 241 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7261 (tm-30) REVERT: I 244 ASP cc_start: 0.7251 (p0) cc_final: 0.7001 (p0) REVERT: I 280 ASN cc_start: 0.7152 (m-40) cc_final: 0.6772 (m110) REVERT: I 316 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7405 (mm-30) REVERT: I 325 MET cc_start: 0.6091 (ppp) cc_final: 0.5624 (ppp) outliers start: 101 outliers final: 81 residues processed: 638 average time/residue: 0.2010 time to fit residues: 209.6302 Evaluate side-chains 636 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 547 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 236 THR 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 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 50 THR 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 100 THR Chi-restraints excluded: chain D residue 160 HIS 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 63 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 41 GLN 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 202 THR 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 167 GLU Chi-restraints excluded: chain N residue 299 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 159 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 330 ILE 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 R residue 34 ILE 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 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL 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 246 GLN 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 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 57 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 403 optimal weight: 0.0040 chunk 472 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 418 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 478 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 chunk 249 optimal weight: 0.9990 overall best weight: 0.5854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 10 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092480 restraints weight = 86462.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094751 restraints weight = 43767.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096235 restraints weight = 27297.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097179 restraints weight = 19766.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097756 restraints weight = 15993.934| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40029 Z= 0.117 Angle : 0.646 15.715 54328 Z= 0.316 Chirality : 0.044 0.236 6016 Planarity : 0.004 0.065 6988 Dihedral : 7.457 157.037 5545 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.40 % Allowed : 21.35 % Favored : 76.25 % 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 aren not related in a simple way. whole: 0.27 (0.13), residues: 4875 helix: 1.08 (0.12), residues: 1842 sheet: -0.41 (0.17), residues: 947 loop : -0.22 (0.15), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 167 TYR 0.025 0.001 TYR I 218 PHE 0.021 0.001 PHE B 24 TRP 0.026 0.001 TRP G 129 HIS 0.007 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00270 (40028) covalent geometry : angle 0.64607 (54326) SS BOND : bond 0.00441 ( 1) SS BOND : angle 1.98215 ( 2) hydrogen bonds : bond 0.03382 ( 1733) hydrogen bonds : angle 4.76889 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6887.40 seconds wall clock time: 119 minutes 30.54 seconds (7170.54 seconds total)