Starting phenix.real_space_refine on Thu Mar 5 16:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqx_21360/03_2026/6vqx_21360.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 23 5.16 5 C 14561 2.51 5 N 4363 2.21 5 O 4690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23696 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 737 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3364 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 397} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2395 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2579 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2577 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2589 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2573 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2576 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 763 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 169, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1125 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 215 Planarities with less than four sites: {'ASP:plan': 11, 'HIS:plan': 8, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 402 Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.65, per 1000 atoms: 0.24 Number of scatterers: 23696 At special positions: 0 Unit cell: (131.44, 146.28, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 59 15.00 O 4690 8.00 N 4363 7.00 C 14561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 38 sheets defined 30.1% alpha, 18.0% beta 1 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.651A pdb=" N ALA A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.616A pdb=" N ALA A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.523A pdb=" N HIS A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 68 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.612A pdb=" N ALA A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 3.531A pdb=" N PHE B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.772A pdb=" N ARG B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.604A pdb=" N THR B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 47' Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.658A pdb=" N GLU B 99 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 100' Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.905A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.539A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.698A pdb=" N LYS B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.615A pdb=" N ASN B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 251 " --> pdb=" O PRO B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 251' Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.680A pdb=" N ARG B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 removed outlier: 3.780A pdb=" N ALA B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.924A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 431 removed outlier: 3.643A pdb=" N GLU B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.925A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 122 through 135 removed outlier: 3.510A pdb=" N GLN C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 removed outlier: 3.708A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.110A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.703A pdb=" N ASP C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 212' Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.933A pdb=" N LEU C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.895A pdb=" N ASN D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.521A pdb=" N HIS D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 344 " --> pdb=" O GLN D 340 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 347 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 348 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.718A pdb=" N SER E 54 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.562A pdb=" N GLN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 Processing helix chain 'E' and resid 149 through 162 removed outlier: 3.630A pdb=" N HIS E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.629A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.843A pdb=" N ARG E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 331 removed outlier: 3.555A pdb=" N ASP E 327 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 removed outlier: 3.527A pdb=" N HIS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 346 " --> pdb=" O HIS E 342 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 348 " --> pdb=" O VAL E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 81 through 91 removed outlier: 3.542A pdb=" N GLN F 90 " --> pdb=" O ASP F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 Processing helix chain 'F' and resid 149 through 162 removed outlier: 3.631A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.252A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 removed outlier: 3.618A pdb=" N ARG F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 removed outlier: 4.126A pdb=" N LEU F 295 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 331 removed outlier: 3.588A pdb=" N ASP F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.788A pdb=" N HIS F 342 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 344 " --> pdb=" O GLN F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.692A pdb=" N ARG G 51 " --> pdb=" O TRP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.724A pdb=" N HIS G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.743A pdb=" N GLU G 215 " --> pdb=" O ASP G 211 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 337 through 351 removed outlier: 4.926A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G 344 " --> pdb=" O GLN G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 57 removed outlier: 3.639A pdb=" N GLN H 55 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU H 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP H 57 " --> pdb=" O SER H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 57' Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.647A pdb=" N ASP H 146 " --> pdb=" O THR H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.627A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.847A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.614A pdb=" N ILE H 278 " --> pdb=" O HIS H 274 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 331 removed outlier: 3.642A pdb=" N ASP H 327 " --> pdb=" O TYR H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 351 removed outlier: 3.898A pdb=" N HIS H 342 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 344 " --> pdb=" O GLN H 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 348 " --> pdb=" O VAL H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.503A pdb=" N ALA I 53 " --> pdb=" O GLN I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 removed outlier: 3.924A pdb=" N ASP I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 147 Processing helix chain 'I' and resid 149 through 162 removed outlier: 3.508A pdb=" N ARG I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 223 removed outlier: 3.870A pdb=" N LEU I 216 " --> pdb=" O ALA I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 283 removed outlier: 4.083A pdb=" N ARG I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 331 removed outlier: 3.533A pdb=" N LEU I 325 " --> pdb=" O ASP I 321 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN I 328 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 351 removed outlier: 3.617A pdb=" N TYR I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.604A pdb=" N GLN B 64 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.571A pdb=" N HIS B 188 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 278 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.571A pdb=" N HIS B 188 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 278 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE C 279 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA C 257 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C 281 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR C 255 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 283 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP C 247 " --> pdb=" O TRP C 289 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA C 253 " --> pdb=" O TRP C 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.502A pdb=" N ILE B 240 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 81 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS B 242 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N LEU C 83 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.502A pdb=" N ILE B 240 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 81 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS B 242 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N LEU C 83 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU I 249 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.171A pdb=" N GLY C 112 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C 59 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU C 110 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA C 103 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 19 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU C 109 " --> pdb=" O PRO C 13 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 11 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 113 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 9 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C 16 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.430A pdb=" N ALA C 103 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 19 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU C 109 " --> pdb=" O PRO C 13 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 11 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 113 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 9 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 157 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB1, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 38 removed outlier: 4.311A pdb=" N VAL D 227 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA D 175 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 180 " --> pdb=" O TRP D 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.638A pdb=" N ALA D 41 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 63 through 65 removed outlier: 3.791A pdb=" N LYS D 65 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 97 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AB6, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'E' and resid 188 through 195 removed outlier: 6.590A pdb=" N HIS E 182 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 191 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 180 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG E 193 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 178 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP E 195 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 176 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 63 through 69 Processing sheet with id=AB9, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC1, first strand: chain 'F' and resid 37 through 38 removed outlier: 4.113A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 62 through 68 Processing sheet with id=AC4, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.485A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU G 228 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL G 176 " --> pdb=" O ASP G 195 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP G 195 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 178 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG G 193 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 180 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA G 191 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS G 182 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 63 through 68 Processing sheet with id=AC8, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC9, first strand: chain 'G' and resid 305 through 306 removed outlier: 3.661A pdb=" N LYS G 311 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 126 through 127 removed outlier: 3.579A pdb=" N ALA H 126 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 352 " --> pdb=" O PHE H 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.210A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD4, first strand: chain 'H' and resid 62 through 67 removed outlier: 4.587A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 62 through 67 removed outlier: 7.000A pdb=" N ASP H 98 " --> pdb=" O SER H 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 126 through 127 removed outlier: 3.802A pdb=" N LEU I 30 " --> pdb=" O PHE I 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 116 through 117 removed outlier: 3.886A pdb=" N GLU I 230 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 116 through 117 removed outlier: 5.021A pdb=" N ALA I 271 " --> pdb=" O MET I 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 62 through 68 removed outlier: 4.649A pdb=" N ALA I 100 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 305 through 306 removed outlier: 3.537A pdb=" N VAL I 306 " --> pdb=" O LYS I 311 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS I 311 " --> pdb=" O VAL I 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 3 through 5 801 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6853 1.33 - 1.45: 4749 1.45 - 1.58: 12517 1.58 - 1.70: 118 1.70 - 1.82: 35 Bond restraints: 24272 Sorted by residual: bond pdb=" C THR B 350 " pdb=" N PRO B 351 " ideal model delta sigma weight residual 1.335 1.376 -0.041 8.70e-03 1.32e+04 2.18e+01 bond pdb=" C PHE C 152 " pdb=" N PRO C 153 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.28e+00 bond pdb=" CA LEU B 130 " pdb=" C LEU B 130 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.39e-02 5.18e+03 3.86e+00 bond pdb=" CG1 ILE G 278 " pdb=" CD1 ILE G 278 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 bond pdb=" C ALA C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.22e-02 6.72e+03 2.30e+00 ... (remaining 24267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 32769 2.96 - 5.92: 340 5.92 - 8.88: 32 8.88 - 11.84: 6 11.84 - 14.80: 3 Bond angle restraints: 33150 Sorted by residual: angle pdb=" C ARG H 268 " pdb=" N ASP H 269 " pdb=" CA ASP H 269 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C PHE B 307 " pdb=" N LEU B 308 " pdb=" CA LEU B 308 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG C 77 " pdb=" CA ARG C 77 " pdb=" C ARG C 77 " ideal model delta sigma weight residual 114.56 108.93 5.63 1.27e+00 6.20e-01 1.97e+01 angle pdb=" CA LEU B 189 " pdb=" CB LEU B 189 " pdb=" CG LEU B 189 " ideal model delta sigma weight residual 116.30 131.10 -14.80 3.50e+00 8.16e-02 1.79e+01 angle pdb=" CA LEU B 343 " pdb=" CB LEU B 343 " pdb=" CG LEU B 343 " ideal model delta sigma weight residual 116.30 130.88 -14.58 3.50e+00 8.16e-02 1.73e+01 ... (remaining 33145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 14057 31.36 - 62.71: 300 62.71 - 94.07: 75 94.07 - 125.43: 0 125.43 - 156.78: 2 Dihedral angle restraints: 14434 sinusoidal: 6215 harmonic: 8219 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 43.22 156.78 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA TRP F 48 " pdb=" C TRP F 48 " pdb=" N ALA F 49 " pdb=" CA ALA F 49 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" N CYS C 217 " pdb=" CA CYS C 217 " ideal model delta harmonic sigma weight residual 180.00 141.51 38.49 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 14431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3278 0.082 - 0.163: 333 0.163 - 0.245: 11 0.245 - 0.326: 4 0.326 - 0.408: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CB ILE G 285 " pdb=" CA ILE G 285 " pdb=" CG1 ILE G 285 " pdb=" CG2 ILE G 285 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL C 249 " pdb=" CA VAL C 249 " pdb=" CG1 VAL C 249 " pdb=" CG2 VAL C 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3624 not shown) Planarity restraints: 4215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 249 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO C 250 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 71 " 0.043 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO B 72 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 329 " -0.020 2.00e-02 2.50e+03 1.60e-02 6.37e+00 pdb=" CG TRP E 329 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 329 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 329 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 329 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 329 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 329 " -0.002 2.00e-02 2.50e+03 ... (remaining 4212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1429 2.72 - 3.27: 22365 3.27 - 3.81: 38818 3.81 - 4.36: 47475 4.36 - 4.90: 79539 Nonbonded interactions: 189626 Sorted by model distance: nonbonded pdb=" CB CYS J 175 " pdb=" OP2 G K 57 " model vdw 2.180 3.440 nonbonded pdb=" O GLU F 301 " pdb=" OH TYR F 343 " model vdw 2.255 3.040 nonbonded pdb=" CD1 LEU B 65 " pdb=" OG SER B 106 " model vdw 2.257 3.460 nonbonded pdb=" OH TYR D 289 " pdb=" O GLY D 296 " model vdw 2.274 3.040 nonbonded pdb=" O SER D 66 " pdb=" O2' U K 47 " model vdw 2.281 3.040 ... (remaining 189621 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 'D' and (resid 24 through 290 or (resid 291 through 293 and (name N or na \ me CA or name C or name O or name CB )) or resid 294 through 356)) selection = (chain 'E' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 290 or (resid 291 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'F' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 356)) selection = (chain 'G' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 290 or (resid 291 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'H' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 291 or (resid 292 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'I' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 291 or (resid 292 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.570 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.061 24272 Z= 0.229 Angle : 0.829 14.798 33150 Z= 0.456 Chirality : 0.049 0.408 3627 Planarity : 0.006 0.067 4215 Dihedral : 13.062 156.782 9240 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.72 % Favored : 91.24 % Rotamer: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.12), residues: 2946 helix: -4.05 (0.08), residues: 840 sheet: -1.21 (0.24), residues: 421 loop : -2.90 (0.12), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 258 TYR 0.022 0.002 TYR F 156 PHE 0.027 0.003 PHE B 211 TRP 0.043 0.004 TRP E 329 HIS 0.011 0.002 HIS G 342 Details of bonding type rmsd covalent geometry : bond 0.00485 (24272) covalent geometry : angle 0.82927 (33150) hydrogen bonds : bond 0.29476 ( 772) hydrogen bonds : angle 9.72797 ( 2209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9136 (p) cc_final: 0.8636 (t) REVERT: A 26 SER cc_start: 0.8626 (t) cc_final: 0.8334 (p) REVERT: A 38 TYR cc_start: 0.9067 (t80) cc_final: 0.8550 (t80) REVERT: A 41 ASP cc_start: 0.8822 (t70) cc_final: 0.7928 (t0) REVERT: B 71 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8594 (mtmt) REVERT: B 82 LEU cc_start: 0.9035 (mt) cc_final: 0.8791 (mt) REVERT: B 118 PHE cc_start: 0.8582 (t80) cc_final: 0.8326 (t80) REVERT: B 153 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7075 (mpt90) REVERT: B 220 GLU cc_start: 0.8632 (tt0) cc_final: 0.8229 (tm-30) REVERT: B 253 GLN cc_start: 0.7031 (tp40) cc_final: 0.6713 (tp-100) REVERT: B 319 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7605 (mpt180) REVERT: B 423 THR cc_start: 0.9011 (m) cc_final: 0.8123 (p) REVERT: B 425 PHE cc_start: 0.9013 (t80) cc_final: 0.8781 (t80) REVERT: C 50 ILE cc_start: 0.9096 (pt) cc_final: 0.8700 (mm) REVERT: C 114 HIS cc_start: 0.6187 (m-70) cc_final: 0.5140 (m170) REVERT: C 116 ASP cc_start: 0.8535 (p0) cc_final: 0.8285 (p0) REVERT: C 159 LEU cc_start: 0.8195 (mp) cc_final: 0.7879 (tt) REVERT: C 170 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8199 (ttp-110) REVERT: C 171 LYS cc_start: 0.9153 (tptt) cc_final: 0.8751 (tppt) REVERT: C 172 ASN cc_start: 0.9078 (t0) cc_final: 0.8708 (t0) REVERT: C 195 GLN cc_start: 0.8378 (tp40) cc_final: 0.8010 (tp40) REVERT: C 198 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8395 (pt0) REVERT: C 211 ASP cc_start: 0.8829 (m-30) cc_final: 0.8011 (t0) REVERT: C 295 VAL cc_start: 0.8686 (t) cc_final: 0.8460 (p) REVERT: D 57 TRP cc_start: 0.8057 (m100) cc_final: 0.7318 (m100) REVERT: D 128 ASN cc_start: 0.8013 (m110) cc_final: 0.7781 (m110) REVERT: D 242 GLU cc_start: 0.7665 (tt0) cc_final: 0.7177 (tm-30) REVERT: D 249 LEU cc_start: 0.7780 (tp) cc_final: 0.7441 (tp) REVERT: D 328 ASN cc_start: 0.8181 (m-40) cc_final: 0.7960 (m-40) REVERT: D 329 TRP cc_start: 0.8594 (t-100) cc_final: 0.8345 (t-100) REVERT: E 35 LYS cc_start: 0.8434 (mptt) cc_final: 0.8131 (mptt) REVERT: E 171 VAL cc_start: 0.9466 (t) cc_final: 0.9222 (m) REVERT: F 78 LYS cc_start: 0.9378 (ttpt) cc_final: 0.9088 (ptpp) REVERT: F 98 ASP cc_start: 0.7834 (m-30) cc_final: 0.7411 (m-30) REVERT: F 260 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8173 (ttmt) REVERT: F 262 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8802 (ttmm) REVERT: G 98 ASP cc_start: 0.7848 (m-30) cc_final: 0.7205 (m-30) REVERT: H 74 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.8013 (mtt-85) REVERT: H 135 LYS cc_start: 0.8900 (tptm) cc_final: 0.8669 (tptm) REVERT: H 211 ASP cc_start: 0.7541 (m-30) cc_final: 0.6624 (m-30) REVERT: H 259 GLN cc_start: 0.7771 (pt0) cc_final: 0.7138 (pm20) REVERT: I 73 ASN cc_start: 0.8579 (m-40) cc_final: 0.8330 (m-40) REVERT: I 135 LYS cc_start: 0.8826 (tptp) cc_final: 0.8264 (tptm) REVERT: I 211 ASP cc_start: 0.8283 (m-30) cc_final: 0.8069 (m-30) outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.2096 time to fit residues: 186.5037 Evaluate side-chains 361 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 148 ASN B 376 GLN B 393 ASN C 21 ASN C 82 ASN C 133 GLN C 149 ASN C 173 GLN C 194 GLN C 269 ASN C 306 HIS D 147 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 HIS F 309 GLN F 318 GLN G 50 GLN G 247 GLN I 138 GLN I 147 GLN I 241 GLN I 340 GLN I 342 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.116628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089260 restraints weight = 55252.227| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.66 r_work: 0.3121 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24272 Z= 0.198 Angle : 0.671 12.556 33150 Z= 0.356 Chirality : 0.042 0.291 3627 Planarity : 0.005 0.051 4215 Dihedral : 14.507 145.262 4178 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.98 % Allowed : 9.79 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.14), residues: 2946 helix: -1.87 (0.14), residues: 872 sheet: -0.71 (0.25), residues: 427 loop : -2.59 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 397 TYR 0.023 0.002 TYR E 156 PHE 0.030 0.002 PHE B 16 TRP 0.025 0.002 TRP E 329 HIS 0.008 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00425 (24272) covalent geometry : angle 0.67139 (33150) hydrogen bonds : bond 0.04702 ( 772) hydrogen bonds : angle 5.61061 ( 2209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 387 time to evaluate : 0.904 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8244 (t) cc_final: 0.7842 (p) REVERT: A 37 TYR cc_start: 0.8991 (t80) cc_final: 0.8768 (t80) REVERT: A 38 TYR cc_start: 0.9226 (t80) cc_final: 0.8876 (t80) REVERT: A 41 ASP cc_start: 0.9166 (t70) cc_final: 0.8756 (t70) REVERT: A 45 ASP cc_start: 0.9210 (t0) cc_final: 0.8807 (t0) REVERT: A 85 LEU cc_start: 0.9364 (mm) cc_final: 0.9115 (mm) REVERT: B 71 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8707 (mtmt) REVERT: B 74 HIS cc_start: 0.9103 (t-90) cc_final: 0.8878 (t-90) REVERT: B 82 LEU cc_start: 0.9071 (mt) cc_final: 0.8736 (mt) REVERT: B 118 PHE cc_start: 0.8969 (t80) cc_final: 0.8752 (t80) REVERT: B 153 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7142 (mpt90) REVERT: B 176 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8752 (mmmt) REVERT: B 220 GLU cc_start: 0.9025 (tt0) cc_final: 0.8501 (tm-30) REVERT: B 242 LYS cc_start: 0.8889 (tttm) cc_final: 0.8511 (mmtm) REVERT: B 281 MET cc_start: 0.6999 (ttt) cc_final: 0.6785 (mmp) REVERT: B 302 ARG cc_start: 0.9056 (mtm110) cc_final: 0.8633 (tpt90) REVERT: B 319 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8164 (mmp80) REVERT: B 389 ASN cc_start: 0.9314 (m110) cc_final: 0.9037 (t0) REVERT: B 393 ASN cc_start: 0.9179 (m-40) cc_final: 0.8929 (m110) REVERT: B 423 THR cc_start: 0.8717 (m) cc_final: 0.8322 (p) REVERT: B 427 GLU cc_start: 0.9152 (mp0) cc_final: 0.8840 (mp0) REVERT: C 50 ILE cc_start: 0.9266 (pt) cc_final: 0.8941 (mm) REVERT: C 116 ASP cc_start: 0.8682 (p0) cc_final: 0.8417 (p0) REVERT: C 126 ILE cc_start: 0.9361 (mm) cc_final: 0.9129 (mt) REVERT: C 166 ASP cc_start: 0.8742 (p0) cc_final: 0.8385 (p0) REVERT: C 170 ARG cc_start: 0.9095 (ttp-110) cc_final: 0.8099 (ttp-110) REVERT: C 171 LYS cc_start: 0.9282 (tptt) cc_final: 0.9029 (tppt) REVERT: C 195 GLN cc_start: 0.8871 (tp40) cc_final: 0.8496 (mt0) REVERT: C 198 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8742 (pp20) REVERT: D 133 ARG cc_start: 0.9213 (ttt-90) cc_final: 0.8973 (ptm160) REVERT: D 135 LYS cc_start: 0.9000 (tmmt) cc_final: 0.8741 (tptt) REVERT: E 33 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8618 (mm-30) REVERT: E 311 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8445 (ptmm) REVERT: F 64 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8617 (mt-10) REVERT: F 86 ASP cc_start: 0.8739 (m-30) cc_final: 0.7963 (t0) REVERT: F 98 ASP cc_start: 0.8495 (m-30) cc_final: 0.7882 (m-30) REVERT: F 146 ASP cc_start: 0.8788 (t70) cc_final: 0.8223 (m-30) REVERT: F 260 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8479 (ttmm) REVERT: F 262 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8732 (ttmm) REVERT: F 269 ASP cc_start: 0.8657 (m-30) cc_final: 0.8033 (t0) REVERT: G 90 GLN cc_start: 0.8738 (mt0) cc_final: 0.8376 (mt0) REVERT: G 95 GLN cc_start: 0.8689 (mt0) cc_final: 0.8473 (mt0) REVERT: G 146 ASP cc_start: 0.8602 (m-30) cc_final: 0.8337 (m-30) REVERT: G 215 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8616 (mt-10) REVERT: H 76 LYS cc_start: 0.8395 (mttp) cc_final: 0.8149 (tppt) REVERT: H 134 ASP cc_start: 0.8863 (p0) cc_final: 0.8598 (p0) REVERT: H 138 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8769 (mm-40) REVERT: I 64 GLU cc_start: 0.8641 (mt-10) cc_final: 0.7959 (mt-10) REVERT: I 67 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9078 (m) REVERT: I 73 ASN cc_start: 0.8939 (m-40) cc_final: 0.8708 (m-40) REVERT: I 137 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9233 (mm) REVERT: I 138 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8051 (pp30) REVERT: I 145 ASN cc_start: 0.8821 (m-40) cc_final: 0.8576 (p0) REVERT: I 202 ARG cc_start: 0.8538 (mtp85) cc_final: 0.7931 (tpt170) REVERT: I 211 ASP cc_start: 0.9023 (m-30) cc_final: 0.8708 (m-30) REVERT: I 260 LYS cc_start: 0.8965 (tttt) cc_final: 0.8594 (tttp) REVERT: I 265 TYR cc_start: 0.9184 (t80) cc_final: 0.8980 (t80) outliers start: 44 outliers final: 23 residues processed: 416 average time/residue: 0.2161 time to fit residues: 127.1681 Evaluate side-chains 349 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 0.0040 chunk 59 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 145 ASN D 147 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089470 restraints weight = 54939.338| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.66 r_work: 0.3125 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24272 Z= 0.155 Angle : 0.602 12.078 33150 Z= 0.315 Chirality : 0.041 0.195 3627 Planarity : 0.004 0.049 4215 Dihedral : 14.306 146.328 4178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.98 % Allowed : 10.64 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 2946 helix: -0.74 (0.17), residues: 877 sheet: -0.53 (0.25), residues: 424 loop : -2.39 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 184 TYR 0.021 0.002 TYR B 235 PHE 0.019 0.001 PHE B 16 TRP 0.024 0.002 TRP C 147 HIS 0.008 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00337 (24272) covalent geometry : angle 0.60158 (33150) hydrogen bonds : bond 0.03812 ( 772) hydrogen bonds : angle 5.10982 ( 2209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 0.708 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8133 (t) cc_final: 0.7649 (p) REVERT: A 37 TYR cc_start: 0.8977 (t80) cc_final: 0.8719 (t80) REVERT: A 38 TYR cc_start: 0.9142 (t80) cc_final: 0.8935 (t80) REVERT: A 41 ASP cc_start: 0.9104 (t70) cc_final: 0.8586 (t70) REVERT: A 85 LEU cc_start: 0.9331 (mm) cc_final: 0.9052 (mm) REVERT: B 71 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8733 (mtpt) REVERT: B 74 HIS cc_start: 0.9067 (t-90) cc_final: 0.8847 (t-90) REVERT: B 82 LEU cc_start: 0.9143 (mt) cc_final: 0.8779 (mt) REVERT: B 118 PHE cc_start: 0.8923 (t80) cc_final: 0.8717 (t80) REVERT: B 153 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7154 (mpt90) REVERT: B 176 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8688 (mmmt) REVERT: B 220 GLU cc_start: 0.9112 (tt0) cc_final: 0.8597 (tm-30) REVERT: B 242 LYS cc_start: 0.8937 (tttm) cc_final: 0.8544 (mmtm) REVERT: B 247 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8515 (mttp) REVERT: B 281 MET cc_start: 0.6816 (ttt) cc_final: 0.6349 (mmp) REVERT: B 302 ARG cc_start: 0.8996 (mtm110) cc_final: 0.8688 (tpt90) REVERT: B 389 ASN cc_start: 0.9312 (m110) cc_final: 0.9046 (t0) REVERT: B 393 ASN cc_start: 0.9172 (m-40) cc_final: 0.8967 (m110) REVERT: B 394 TRP cc_start: 0.8006 (t-100) cc_final: 0.7762 (t-100) REVERT: B 423 THR cc_start: 0.8719 (m) cc_final: 0.8204 (p) REVERT: B 427 GLU cc_start: 0.9251 (mp0) cc_final: 0.8994 (mp0) REVERT: C 50 ILE cc_start: 0.9231 (pt) cc_final: 0.8928 (mm) REVERT: C 126 ILE cc_start: 0.9364 (mm) cc_final: 0.9161 (mt) REVERT: C 166 ASP cc_start: 0.8854 (p0) cc_final: 0.8590 (p0) REVERT: C 170 ARG cc_start: 0.8989 (ttp-110) cc_final: 0.8529 (ttp-110) REVERT: C 171 LYS cc_start: 0.9321 (tptt) cc_final: 0.8948 (tppt) REVERT: C 195 GLN cc_start: 0.8810 (tp40) cc_final: 0.8375 (mt0) REVERT: C 196 HIS cc_start: 0.8754 (t70) cc_final: 0.8553 (t-170) REVERT: C 198 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8729 (pp20) REVERT: C 262 TYR cc_start: 0.8544 (m-80) cc_final: 0.7920 (m-80) REVERT: C 288 GLU cc_start: 0.8898 (tt0) cc_final: 0.8678 (tt0) REVERT: C 308 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: D 135 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8797 (tptt) REVERT: E 33 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8634 (mm-30) REVERT: E 64 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 138 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8542 (mm-40) REVERT: E 184 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7327 (mtp85) REVERT: E 311 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8421 (ptmm) REVERT: F 51 ARG cc_start: 0.8533 (mpt180) cc_final: 0.8287 (mmt-90) REVERT: F 64 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8564 (mt-10) REVERT: F 76 LYS cc_start: 0.8356 (ptmm) cc_final: 0.8112 (ptmm) REVERT: F 86 ASP cc_start: 0.8815 (m-30) cc_final: 0.8053 (t0) REVERT: F 95 GLN cc_start: 0.8547 (tt0) cc_final: 0.8290 (mt0) REVERT: F 98 ASP cc_start: 0.8561 (m-30) cc_final: 0.8028 (m-30) REVERT: F 260 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8409 (ttmt) REVERT: F 268 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8452 (mtm-85) REVERT: F 269 ASP cc_start: 0.8665 (m-30) cc_final: 0.8033 (t0) REVERT: G 90 GLN cc_start: 0.8776 (mt0) cc_final: 0.8382 (mt0) REVERT: G 95 GLN cc_start: 0.8738 (mt0) cc_final: 0.8455 (mt0) REVERT: G 147 GLN cc_start: 0.8153 (pm20) cc_final: 0.7941 (pm20) REVERT: G 332 ARG cc_start: 0.8805 (mpp80) cc_final: 0.7594 (mtm-85) REVERT: H 64 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8336 (mt-10) REVERT: H 76 LYS cc_start: 0.8314 (mttp) cc_final: 0.8088 (tppt) REVERT: H 133 ARG cc_start: 0.8855 (ttm-80) cc_final: 0.8480 (ttm110) REVERT: H 134 ASP cc_start: 0.8851 (p0) cc_final: 0.8493 (p0) REVERT: H 135 LYS cc_start: 0.9295 (tptm) cc_final: 0.9081 (tptm) REVERT: H 138 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8742 (mm-40) REVERT: H 260 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9119 (ttmt) REVERT: I 64 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8173 (mp0) REVERT: I 145 ASN cc_start: 0.8862 (m-40) cc_final: 0.8633 (m110) REVERT: I 202 ARG cc_start: 0.8493 (mtp85) cc_final: 0.7897 (tpt170) REVERT: I 211 ASP cc_start: 0.8988 (m-30) cc_final: 0.8654 (m-30) REVERT: I 255 ASP cc_start: 0.8445 (t70) cc_final: 0.7902 (p0) REVERT: I 260 LYS cc_start: 0.8885 (tttt) cc_final: 0.8637 (tptm) REVERT: I 265 TYR cc_start: 0.9183 (t80) cc_final: 0.8863 (t80) REVERT: I 301 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8440 (mm-30) outliers start: 44 outliers final: 27 residues processed: 368 average time/residue: 0.2070 time to fit residues: 109.1106 Evaluate side-chains 344 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 289 optimal weight: 30.0000 chunk 288 optimal weight: 20.0000 chunk 128 optimal weight: 0.0870 chunk 285 optimal weight: 30.0000 chunk 132 optimal weight: 0.0670 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 200 HIS B 289 HIS ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN C 149 ASN C 196 HIS C 306 HIS D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN F 147 GLN H 226 HIS I 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.115604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088015 restraints weight = 54914.156| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.66 r_work: 0.3096 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24272 Z= 0.180 Angle : 0.595 13.027 33150 Z= 0.312 Chirality : 0.040 0.175 3627 Planarity : 0.004 0.048 4215 Dihedral : 14.235 147.766 4178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.11 % Allowed : 11.63 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.15), residues: 2946 helix: -0.20 (0.18), residues: 884 sheet: -0.38 (0.25), residues: 439 loop : -2.30 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 184 TYR 0.025 0.002 TYR B 235 PHE 0.024 0.001 PHE A 6 TRP 0.035 0.002 TRP C 147 HIS 0.008 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00391 (24272) covalent geometry : angle 0.59540 (33150) hydrogen bonds : bond 0.03566 ( 772) hydrogen bonds : angle 4.89825 ( 2209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 0.910 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: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9154 (p) cc_final: 0.8409 (p) REVERT: A 16 GLN cc_start: 0.8559 (mp10) cc_final: 0.7850 (mp-120) REVERT: A 19 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8430 (tm-30) REVERT: A 26 SER cc_start: 0.8075 (t) cc_final: 0.7584 (p) REVERT: A 37 TYR cc_start: 0.9001 (t80) cc_final: 0.8753 (t80) REVERT: A 38 TYR cc_start: 0.9261 (t80) cc_final: 0.8819 (t80) REVERT: A 41 ASP cc_start: 0.9161 (t70) cc_final: 0.8593 (t70) REVERT: A 86 GLN cc_start: 0.8952 (pt0) cc_final: 0.8664 (pt0) REVERT: B 74 HIS cc_start: 0.9067 (t-90) cc_final: 0.8760 (t-90) REVERT: B 82 LEU cc_start: 0.9176 (mt) cc_final: 0.8796 (mt) REVERT: B 118 PHE cc_start: 0.8946 (t80) cc_final: 0.8684 (t80) REVERT: B 153 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7180 (mpt90) REVERT: B 220 GLU cc_start: 0.9115 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 226 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 242 LYS cc_start: 0.8974 (tttm) cc_final: 0.8571 (mmtm) REVERT: B 247 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8658 (mttp) REVERT: B 281 MET cc_start: 0.6806 (ttt) cc_final: 0.6512 (mmp) REVERT: B 302 ARG cc_start: 0.9048 (mtm110) cc_final: 0.8758 (tpt90) REVERT: B 389 ASN cc_start: 0.9323 (m110) cc_final: 0.9007 (t0) REVERT: B 423 THR cc_start: 0.8743 (m) cc_final: 0.8282 (m) REVERT: B 427 GLU cc_start: 0.9273 (mp0) cc_final: 0.9007 (mp0) REVERT: C 50 ILE cc_start: 0.9240 (pt) cc_final: 0.8956 (mm) REVERT: C 89 ASN cc_start: 0.9391 (m-40) cc_final: 0.8880 (m-40) REVERT: C 166 ASP cc_start: 0.8812 (p0) cc_final: 0.8554 (p0) REVERT: C 170 ARG cc_start: 0.9054 (ttp-110) cc_final: 0.8616 (ttp-110) REVERT: C 171 LYS cc_start: 0.9328 (tptt) cc_final: 0.9112 (tppt) REVERT: C 195 GLN cc_start: 0.8796 (tp40) cc_final: 0.8279 (mt0) REVERT: C 198 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8821 (pp20) REVERT: C 262 TYR cc_start: 0.8470 (m-80) cc_final: 0.8071 (m-80) REVERT: C 288 GLU cc_start: 0.8904 (tt0) cc_final: 0.8692 (tt0) REVERT: C 308 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: D 40 ASP cc_start: 0.8445 (m-30) cc_final: 0.8134 (m-30) REVERT: D 63 ARG cc_start: 0.8264 (ptm160) cc_final: 0.8057 (ptm160) REVERT: D 277 LYS cc_start: 0.9297 (tmtm) cc_final: 0.9059 (tptp) REVERT: D 329 TRP cc_start: 0.9009 (t60) cc_final: 0.8784 (t60) REVERT: E 33 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8586 (mm-30) REVERT: E 64 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7575 (mm-30) REVERT: E 184 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7309 (mtp85) REVERT: E 311 LYS cc_start: 0.8718 (ptmm) cc_final: 0.8412 (ptmm) REVERT: F 64 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8525 (mt-10) REVERT: F 76 LYS cc_start: 0.8338 (ptmm) cc_final: 0.8109 (ptmm) REVERT: F 86 ASP cc_start: 0.8831 (m-30) cc_final: 0.7564 (t0) REVERT: F 90 GLN cc_start: 0.8566 (mp10) cc_final: 0.8084 (mm110) REVERT: F 98 ASP cc_start: 0.8524 (m-30) cc_final: 0.8055 (m-30) REVERT: F 260 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8458 (ttmt) REVERT: F 268 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: F 269 ASP cc_start: 0.8706 (m-30) cc_final: 0.8030 (t0) REVERT: G 90 GLN cc_start: 0.8811 (mt0) cc_final: 0.8319 (mt0) REVERT: G 95 GLN cc_start: 0.8809 (mt0) cc_final: 0.8609 (mt0) REVERT: G 135 LYS cc_start: 0.9320 (tppt) cc_final: 0.8998 (tptm) REVERT: G 298 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8363 (tp) REVERT: G 332 ARG cc_start: 0.8713 (mpp80) cc_final: 0.8026 (mtm-85) REVERT: H 76 LYS cc_start: 0.8390 (mttp) cc_final: 0.8136 (tppt) REVERT: H 133 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8485 (ttm110) REVERT: I 64 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8153 (mp0) REVERT: I 145 ASN cc_start: 0.8878 (m-40) cc_final: 0.8641 (m110) REVERT: I 202 ARG cc_start: 0.8548 (mtp85) cc_final: 0.7965 (tpt170) REVERT: I 211 ASP cc_start: 0.9025 (m-30) cc_final: 0.8709 (m-30) REVERT: I 255 ASP cc_start: 0.8462 (t70) cc_final: 0.7924 (p0) REVERT: I 260 LYS cc_start: 0.8908 (tttt) cc_final: 0.8631 (tptm) REVERT: I 265 TYR cc_start: 0.9197 (t80) cc_final: 0.8880 (t80) REVERT: I 301 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8261 (mm-30) REVERT: I 317 LYS cc_start: 0.8864 (pptt) cc_final: 0.8548 (pptt) outliers start: 47 outliers final: 31 residues processed: 369 average time/residue: 0.2069 time to fit residues: 110.0708 Evaluate side-chains 344 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 172 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 284 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 196 HIS C 306 HIS D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086942 restraints weight = 54778.305| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.65 r_work: 0.3078 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24272 Z= 0.199 Angle : 0.604 13.103 33150 Z= 0.317 Chirality : 0.041 0.179 3627 Planarity : 0.004 0.059 4215 Dihedral : 14.208 147.450 4178 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.51 % Allowed : 12.35 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.15), residues: 2946 helix: 0.04 (0.18), residues: 885 sheet: -0.22 (0.25), residues: 439 loop : -2.24 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 77 TYR 0.024 0.002 TYR D 132 PHE 0.018 0.001 PHE B 16 TRP 0.033 0.002 TRP C 147 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00432 (24272) covalent geometry : angle 0.60380 (33150) hydrogen bonds : bond 0.03530 ( 772) hydrogen bonds : angle 4.84494 ( 2209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 0.794 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: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9096 (p) cc_final: 0.8808 (p) REVERT: A 16 GLN cc_start: 0.8498 (mp10) cc_final: 0.8249 (mp-120) REVERT: A 19 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8484 (tm-30) REVERT: A 26 SER cc_start: 0.8105 (t) cc_final: 0.7598 (p) REVERT: A 37 TYR cc_start: 0.9009 (t80) cc_final: 0.8764 (t80) REVERT: A 38 TYR cc_start: 0.9294 (t80) cc_final: 0.8819 (t80) REVERT: A 41 ASP cc_start: 0.9157 (t70) cc_final: 0.8540 (t70) REVERT: A 64 HIS cc_start: 0.8875 (m-70) cc_final: 0.8467 (m-70) REVERT: A 77 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8105 (tpp80) REVERT: A 86 GLN cc_start: 0.8942 (pt0) cc_final: 0.8444 (pm20) REVERT: B 74 HIS cc_start: 0.9116 (t-90) cc_final: 0.8825 (t-90) REVERT: B 82 LEU cc_start: 0.9185 (mt) cc_final: 0.8794 (mt) REVERT: B 118 PHE cc_start: 0.8974 (t80) cc_final: 0.8630 (t80) REVERT: B 153 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7230 (mpt90) REVERT: B 220 GLU cc_start: 0.9100 (tt0) cc_final: 0.8623 (tp30) REVERT: B 247 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8681 (mttp) REVERT: B 302 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8802 (tpt90) REVERT: B 308 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.5883 (pp) REVERT: B 319 ARG cc_start: 0.8724 (mmp80) cc_final: 0.8369 (mpt180) REVERT: B 397 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8158 (ptt-90) REVERT: B 423 THR cc_start: 0.8770 (m) cc_final: 0.8194 (m) REVERT: B 427 GLU cc_start: 0.9351 (mp0) cc_final: 0.9113 (mp0) REVERT: C 50 ILE cc_start: 0.9258 (pt) cc_final: 0.8963 (mm) REVERT: C 77 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7150 (tpt90) REVERT: C 166 ASP cc_start: 0.8753 (p0) cc_final: 0.8552 (p0) REVERT: C 170 ARG cc_start: 0.9058 (ttp-110) cc_final: 0.8558 (ttp-110) REVERT: C 195 GLN cc_start: 0.8766 (tp40) cc_final: 0.8422 (mt0) REVERT: C 198 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8806 (pp20) REVERT: C 262 TYR cc_start: 0.8538 (m-80) cc_final: 0.8155 (m-80) REVERT: C 288 GLU cc_start: 0.8920 (tt0) cc_final: 0.8679 (tt0) REVERT: C 308 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7278 (pp20) REVERT: D 40 ASP cc_start: 0.8420 (m-30) cc_final: 0.8067 (m-30) REVERT: D 63 ARG cc_start: 0.8327 (ptm160) cc_final: 0.8118 (ptm160) REVERT: D 147 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: D 301 GLU cc_start: 0.9023 (pt0) cc_final: 0.8605 (mp0) REVERT: E 33 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8580 (mm-30) REVERT: E 64 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7585 (mm-30) REVERT: E 138 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8586 (mm-40) REVERT: E 184 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7289 (mtp85) REVERT: E 311 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8384 (ptmm) REVERT: F 64 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8515 (tt0) REVERT: F 76 LYS cc_start: 0.8353 (ptmm) cc_final: 0.8119 (ptmm) REVERT: F 86 ASP cc_start: 0.8877 (m-30) cc_final: 0.8078 (t0) REVERT: F 95 GLN cc_start: 0.8455 (mt0) cc_final: 0.8251 (mt0) REVERT: F 98 ASP cc_start: 0.8527 (m-30) cc_final: 0.8083 (m-30) REVERT: F 260 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8456 (ttmm) REVERT: F 268 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8433 (mtm-85) REVERT: F 269 ASP cc_start: 0.8714 (m-30) cc_final: 0.8042 (t0) REVERT: G 90 GLN cc_start: 0.8808 (mt0) cc_final: 0.8311 (mt0) REVERT: G 95 GLN cc_start: 0.8801 (mt0) cc_final: 0.8592 (mt0) REVERT: G 135 LYS cc_start: 0.9344 (tppt) cc_final: 0.9030 (tptm) REVERT: G 298 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8387 (tp) REVERT: H 51 ARG cc_start: 0.4274 (mmt-90) cc_final: 0.2486 (mpt90) REVERT: H 76 LYS cc_start: 0.8388 (mttp) cc_final: 0.8159 (tppt) REVERT: H 260 LYS cc_start: 0.9353 (ttmt) cc_final: 0.9129 (ttmt) REVERT: H 333 ASP cc_start: 0.8818 (t0) cc_final: 0.8600 (t0) REVERT: I 64 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8132 (mp0) REVERT: I 145 ASN cc_start: 0.8859 (m-40) cc_final: 0.8609 (m110) REVERT: I 146 ASP cc_start: 0.8695 (t0) cc_final: 0.8400 (m-30) REVERT: I 202 ARG cc_start: 0.8525 (mtp85) cc_final: 0.7945 (tpt170) REVERT: I 211 ASP cc_start: 0.9004 (m-30) cc_final: 0.8684 (m-30) REVERT: I 255 ASP cc_start: 0.8505 (t70) cc_final: 0.8010 (p0) REVERT: I 260 LYS cc_start: 0.8884 (tttt) cc_final: 0.8596 (tppp) REVERT: I 265 TYR cc_start: 0.9197 (t80) cc_final: 0.8884 (t80) REVERT: I 301 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8233 (mm-30) REVERT: I 317 LYS cc_start: 0.8811 (pptt) cc_final: 0.8461 (pptt) outliers start: 56 outliers final: 34 residues processed: 356 average time/residue: 0.2129 time to fit residues: 107.8703 Evaluate side-chains 342 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 235 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 86 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 192 optimal weight: 0.0670 chunk 33 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 HIS C 149 ASN D 101 ASN ** D 340 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 = 0.3771 r_free = 0.3771 target = 0.117327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089976 restraints weight = 54866.796| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.65 r_work: 0.3128 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24272 Z= 0.123 Angle : 0.555 11.384 33150 Z= 0.289 Chirality : 0.039 0.177 3627 Planarity : 0.004 0.047 4215 Dihedral : 14.037 149.340 4178 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.25 % Allowed : 13.25 % Favored : 84.51 % 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 are not related in a simple way. whole: -1.51 (0.15), residues: 2946 helix: 0.37 (0.18), residues: 876 sheet: -0.02 (0.25), residues: 442 loop : -2.17 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 184 TYR 0.023 0.002 TYR D 132 PHE 0.011 0.001 PHE D 165 TRP 0.026 0.001 TRP B 414 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00270 (24272) covalent geometry : angle 0.55506 (33150) hydrogen bonds : bond 0.03025 ( 772) hydrogen bonds : angle 4.60653 ( 2209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 0.827 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: symmetry clash REVERT: A 13 THR cc_start: 0.9084 (p) cc_final: 0.8158 (p) REVERT: A 16 GLN cc_start: 0.8556 (mp10) cc_final: 0.7798 (mp-120) REVERT: A 19 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8534 (tm-30) REVERT: A 26 SER cc_start: 0.8046 (t) cc_final: 0.7567 (p) REVERT: A 37 TYR cc_start: 0.9005 (t80) cc_final: 0.8733 (t80) REVERT: A 38 TYR cc_start: 0.9260 (t80) cc_final: 0.8796 (t80) REVERT: A 41 ASP cc_start: 0.9118 (t70) cc_final: 0.8536 (t70) REVERT: A 64 HIS cc_start: 0.8875 (m-70) cc_final: 0.8458 (m-70) REVERT: A 77 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7978 (tpp80) REVERT: A 86 GLN cc_start: 0.8944 (pt0) cc_final: 0.8400 (pm20) REVERT: B 74 HIS cc_start: 0.9105 (t-90) cc_final: 0.8829 (t-90) REVERT: B 82 LEU cc_start: 0.9142 (mt) cc_final: 0.8785 (mt) REVERT: B 118 PHE cc_start: 0.8906 (t80) cc_final: 0.8626 (t80) REVERT: B 153 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7235 (mpt90) REVERT: B 220 GLU cc_start: 0.9154 (tt0) cc_final: 0.8777 (tm-30) REVERT: B 247 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8568 (mttp) REVERT: B 302 ARG cc_start: 0.9087 (mtm110) cc_final: 0.8780 (tpt90) REVERT: B 308 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.5757 (pp) REVERT: B 319 ARG cc_start: 0.8690 (mmp80) cc_final: 0.8351 (mpt180) REVERT: B 423 THR cc_start: 0.8799 (m) cc_final: 0.8151 (m) REVERT: B 427 GLU cc_start: 0.9371 (mp0) cc_final: 0.9022 (mp0) REVERT: C 50 ILE cc_start: 0.9210 (pt) cc_final: 0.8981 (mm) REVERT: C 77 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7174 (tpt90) REVERT: C 114 HIS cc_start: 0.7224 (m-70) cc_final: 0.6639 (m-70) REVERT: C 166 ASP cc_start: 0.8736 (p0) cc_final: 0.8535 (p0) REVERT: C 170 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8566 (ttp-110) REVERT: C 262 TYR cc_start: 0.8471 (m-80) cc_final: 0.8095 (m-80) REVERT: C 308 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: D 63 ARG cc_start: 0.8372 (ptm160) cc_final: 0.8157 (ptm160) REVERT: D 301 GLU cc_start: 0.8907 (pt0) cc_final: 0.8449 (mp0) REVERT: E 33 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8457 (mm-30) REVERT: E 64 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7603 (tp30) REVERT: E 184 ARG cc_start: 0.7343 (mtp85) cc_final: 0.7051 (mtp85) REVERT: E 311 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8367 (ptmm) REVERT: F 64 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8512 (tt0) REVERT: F 76 LYS cc_start: 0.8361 (ptmm) cc_final: 0.8106 (ptmm) REVERT: F 86 ASP cc_start: 0.8773 (m-30) cc_final: 0.8044 (t0) REVERT: F 98 ASP cc_start: 0.8509 (m-30) cc_final: 0.8029 (m-30) REVERT: F 260 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8396 (ttmm) REVERT: F 268 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8489 (mtm-85) REVERT: F 269 ASP cc_start: 0.8708 (m-30) cc_final: 0.8072 (t0) REVERT: G 90 GLN cc_start: 0.8807 (mt0) cc_final: 0.8304 (mt0) REVERT: G 95 GLN cc_start: 0.8784 (mt0) cc_final: 0.8513 (mt0) REVERT: G 135 LYS cc_start: 0.9322 (tppt) cc_final: 0.9012 (tptm) REVERT: G 298 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8364 (tp) REVERT: H 28 SER cc_start: 0.9476 (m) cc_final: 0.9108 (t) REVERT: H 51 ARG cc_start: 0.4196 (mmt-90) cc_final: 0.2475 (mpt90) REVERT: H 86 ASP cc_start: 0.8735 (m-30) cc_final: 0.8417 (m-30) REVERT: H 133 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8416 (ttm110) REVERT: H 135 LYS cc_start: 0.9363 (tptm) cc_final: 0.9116 (tptm) REVERT: H 138 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8292 (mm-40) REVERT: H 260 LYS cc_start: 0.9312 (ttmt) cc_final: 0.9079 (ttmt) REVERT: H 333 ASP cc_start: 0.8829 (t0) cc_final: 0.8500 (t0) REVERT: I 64 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8157 (mp0) REVERT: I 67 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9081 (m) REVERT: I 145 ASN cc_start: 0.8824 (m-40) cc_final: 0.8561 (m110) REVERT: I 146 ASP cc_start: 0.8655 (t0) cc_final: 0.8401 (m-30) REVERT: I 202 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8013 (tpt170) REVERT: I 211 ASP cc_start: 0.8945 (m-30) cc_final: 0.8608 (m-30) REVERT: I 255 ASP cc_start: 0.8467 (t70) cc_final: 0.8061 (p0) REVERT: I 260 LYS cc_start: 0.8830 (tttt) cc_final: 0.8534 (tppp) REVERT: I 301 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8217 (mm-30) REVERT: I 317 LYS cc_start: 0.8857 (pptt) cc_final: 0.8519 (pptt) REVERT: I 334 GLU cc_start: 0.8905 (tp30) cc_final: 0.8573 (tm-30) outliers start: 50 outliers final: 26 residues processed: 369 average time/residue: 0.2057 time to fit residues: 109.2161 Evaluate side-chains 335 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087072 restraints weight = 54767.188| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.66 r_work: 0.3075 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24272 Z= 0.199 Angle : 0.602 12.901 33150 Z= 0.313 Chirality : 0.041 0.181 3627 Planarity : 0.004 0.056 4215 Dihedral : 14.059 149.522 4178 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.16 % Allowed : 14.10 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 2946 helix: 0.39 (0.18), residues: 885 sheet: 0.03 (0.25), residues: 438 loop : -2.15 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 193 TYR 0.025 0.002 TYR B 235 PHE 0.015 0.001 PHE B 16 TRP 0.031 0.002 TRP D 57 HIS 0.008 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00435 (24272) covalent geometry : angle 0.60190 (33150) hydrogen bonds : bond 0.03356 ( 772) hydrogen bonds : angle 4.71472 ( 2209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 0.905 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 13 THR cc_start: 0.9105 (p) cc_final: 0.8133 (p) REVERT: A 16 GLN cc_start: 0.8503 (mp10) cc_final: 0.7735 (mp-120) REVERT: A 19 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8570 (tm-30) REVERT: A 26 SER cc_start: 0.8070 (t) cc_final: 0.7608 (p) REVERT: A 37 TYR cc_start: 0.9028 (t80) cc_final: 0.8777 (t80) REVERT: A 38 TYR cc_start: 0.9320 (t80) cc_final: 0.8858 (t80) REVERT: A 41 ASP cc_start: 0.9124 (t70) cc_final: 0.8664 (t70) REVERT: B 74 HIS cc_start: 0.9111 (t-90) cc_final: 0.8864 (t70) REVERT: B 82 LEU cc_start: 0.9191 (mt) cc_final: 0.8789 (mt) REVERT: B 104 LEU cc_start: 0.9410 (tt) cc_final: 0.9056 (mp) REVERT: B 118 PHE cc_start: 0.8961 (t80) cc_final: 0.8624 (t80) REVERT: B 220 GLU cc_start: 0.9130 (tt0) cc_final: 0.8631 (tp30) REVERT: B 263 TRP cc_start: 0.8547 (m100) cc_final: 0.8318 (m100) REVERT: B 302 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8811 (tpt90) REVERT: B 308 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.5730 (pp) REVERT: B 319 ARG cc_start: 0.8698 (mmp80) cc_final: 0.8346 (mpt180) REVERT: B 332 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9015 (tm-30) REVERT: B 423 THR cc_start: 0.8820 (m) cc_final: 0.8159 (m) REVERT: B 427 GLU cc_start: 0.9328 (mp0) cc_final: 0.9004 (mp0) REVERT: C 50 ILE cc_start: 0.9251 (pt) cc_final: 0.9008 (mm) REVERT: C 77 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7473 (mmm160) REVERT: C 85 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8017 (tpp80) REVERT: C 170 ARG cc_start: 0.9084 (ttp-110) cc_final: 0.8659 (ttp-110) REVERT: C 262 TYR cc_start: 0.8587 (m-80) cc_final: 0.8166 (m-80) REVERT: D 40 ASP cc_start: 0.8448 (m-30) cc_final: 0.8216 (m-30) REVERT: D 301 GLU cc_start: 0.8948 (pt0) cc_final: 0.8502 (pm20) REVERT: E 33 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8561 (mm-30) REVERT: E 64 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7629 (mm-30) REVERT: E 95 GLN cc_start: 0.8367 (tt0) cc_final: 0.7667 (pt0) REVERT: E 138 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8564 (mm-40) REVERT: E 184 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7256 (mtp85) REVERT: F 64 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8493 (tt0) REVERT: F 76 LYS cc_start: 0.8367 (ptmm) cc_final: 0.8117 (ptmm) REVERT: F 86 ASP cc_start: 0.8812 (m-30) cc_final: 0.8051 (t0) REVERT: F 98 ASP cc_start: 0.8465 (m-30) cc_final: 0.8061 (m-30) REVERT: F 260 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8409 (ttmm) REVERT: F 268 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8507 (mtm-85) REVERT: F 269 ASP cc_start: 0.8736 (m-30) cc_final: 0.8084 (t0) REVERT: G 90 GLN cc_start: 0.8799 (mt0) cc_final: 0.8223 (mp10) REVERT: G 95 GLN cc_start: 0.8782 (mt0) cc_final: 0.8464 (mt0) REVERT: G 135 LYS cc_start: 0.9345 (tppt) cc_final: 0.9039 (tptm) REVERT: G 193 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8371 (mmt90) REVERT: H 28 SER cc_start: 0.9507 (m) cc_final: 0.9145 (t) REVERT: H 51 ARG cc_start: 0.4519 (mmt-90) cc_final: 0.2400 (mpt90) REVERT: H 86 ASP cc_start: 0.8780 (m-30) cc_final: 0.8497 (m-30) REVERT: H 133 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.8476 (ttm110) REVERT: H 311 LYS cc_start: 0.9195 (pttt) cc_final: 0.8770 (ptmm) REVERT: H 333 ASP cc_start: 0.8954 (t0) cc_final: 0.8592 (t0) REVERT: I 64 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8096 (mp0) REVERT: I 145 ASN cc_start: 0.8851 (m-40) cc_final: 0.8606 (m110) REVERT: I 146 ASP cc_start: 0.8665 (t0) cc_final: 0.8403 (m-30) REVERT: I 202 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8008 (tpt170) REVERT: I 211 ASP cc_start: 0.8956 (m-30) cc_final: 0.8622 (m-30) REVERT: I 255 ASP cc_start: 0.8493 (t70) cc_final: 0.8095 (p0) REVERT: I 260 LYS cc_start: 0.8900 (tttt) cc_final: 0.8564 (tppp) REVERT: I 265 TYR cc_start: 0.9194 (t80) cc_final: 0.8893 (t80) REVERT: I 301 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8168 (mm-30) REVERT: I 317 LYS cc_start: 0.8868 (pptt) cc_final: 0.8640 (pptt) outliers start: 48 outliers final: 31 residues processed: 342 average time/residue: 0.2081 time to fit residues: 102.2359 Evaluate side-chains 332 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 230 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087288 restraints weight = 54894.337| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.65 r_work: 0.3084 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24272 Z= 0.179 Angle : 0.613 16.969 33150 Z= 0.318 Chirality : 0.041 0.183 3627 Planarity : 0.004 0.067 4215 Dihedral : 14.043 149.113 4178 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.29 % Allowed : 14.59 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 2946 helix: 0.45 (0.18), residues: 874 sheet: 0.02 (0.25), residues: 448 loop : -2.09 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 184 TYR 0.027 0.002 TYR B 235 PHE 0.014 0.001 PHE B 16 TRP 0.061 0.002 TRP D 57 HIS 0.008 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00394 (24272) covalent geometry : angle 0.61267 (33150) hydrogen bonds : bond 0.03311 ( 772) hydrogen bonds : angle 4.65228 ( 2209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.980 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: symmetry clash REVERT: A 13 THR cc_start: 0.9127 (p) cc_final: 0.8926 (p) REVERT: A 16 GLN cc_start: 0.8509 (mp10) cc_final: 0.8296 (mm-40) REVERT: A 19 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8560 (tm-30) REVERT: A 26 SER cc_start: 0.8033 (t) cc_final: 0.7575 (p) REVERT: A 37 TYR cc_start: 0.9020 (t80) cc_final: 0.8730 (t80) REVERT: A 38 TYR cc_start: 0.9298 (t80) cc_final: 0.8883 (t80) REVERT: A 41 ASP cc_start: 0.9114 (t70) cc_final: 0.8324 (t0) REVERT: B 74 HIS cc_start: 0.9110 (t-90) cc_final: 0.8860 (t70) REVERT: B 82 LEU cc_start: 0.9186 (mt) cc_final: 0.8789 (mt) REVERT: B 104 LEU cc_start: 0.9423 (tt) cc_final: 0.9015 (mp) REVERT: B 118 PHE cc_start: 0.8932 (t80) cc_final: 0.8584 (t80) REVERT: B 123 LEU cc_start: 0.8384 (mt) cc_final: 0.8130 (pp) REVERT: B 220 GLU cc_start: 0.9146 (tt0) cc_final: 0.8637 (tp30) REVERT: B 242 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8717 (tppt) REVERT: B 308 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5687 (pp) REVERT: B 319 ARG cc_start: 0.8735 (mmp80) cc_final: 0.8377 (mpt180) REVERT: B 332 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9047 (tm-30) REVERT: C 50 ILE cc_start: 0.9262 (pt) cc_final: 0.9037 (mm) REVERT: C 77 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7455 (mmm160) REVERT: C 170 ARG cc_start: 0.9105 (ttp-110) cc_final: 0.8761 (ttp-110) REVERT: C 198 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8811 (pp20) REVERT: C 262 TYR cc_start: 0.8580 (m-80) cc_final: 0.8203 (m-80) REVERT: D 63 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7894 (ptm160) REVERT: D 301 GLU cc_start: 0.8949 (pt0) cc_final: 0.8521 (pm20) REVERT: E 33 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8529 (mm-30) REVERT: E 64 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 95 GLN cc_start: 0.8442 (mt0) cc_final: 0.7772 (pt0) REVERT: E 138 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8563 (mm-40) REVERT: E 184 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7220 (mtp85) REVERT: F 64 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8484 (tt0) REVERT: F 86 ASP cc_start: 0.8827 (m-30) cc_final: 0.8062 (t0) REVERT: F 98 ASP cc_start: 0.8454 (m-30) cc_final: 0.8050 (m-30) REVERT: F 260 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8401 (ttmm) REVERT: F 268 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8513 (mtm-85) REVERT: F 269 ASP cc_start: 0.8728 (m-30) cc_final: 0.8078 (t0) REVERT: G 90 GLN cc_start: 0.8792 (mt0) cc_final: 0.8236 (mp10) REVERT: G 95 GLN cc_start: 0.8773 (mt0) cc_final: 0.8448 (mt0) REVERT: G 135 LYS cc_start: 0.9353 (tppt) cc_final: 0.9055 (tptm) REVERT: G 298 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8378 (tp) REVERT: H 28 SER cc_start: 0.9503 (m) cc_final: 0.9142 (t) REVERT: H 51 ARG cc_start: 0.4696 (mmt-90) cc_final: 0.1002 (mtt-85) REVERT: H 311 LYS cc_start: 0.9211 (pttt) cc_final: 0.8796 (ptmm) REVERT: H 333 ASP cc_start: 0.8954 (t0) cc_final: 0.8717 (t0) REVERT: I 64 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8066 (mp0) REVERT: I 72 SER cc_start: 0.9197 (p) cc_final: 0.8757 (t) REVERT: I 145 ASN cc_start: 0.8856 (m-40) cc_final: 0.8620 (m110) REVERT: I 146 ASP cc_start: 0.8639 (t0) cc_final: 0.8405 (m-30) REVERT: I 202 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8025 (tpt170) REVERT: I 211 ASP cc_start: 0.8945 (m-30) cc_final: 0.8611 (m-30) REVERT: I 255 ASP cc_start: 0.8444 (t70) cc_final: 0.7947 (p0) REVERT: I 260 LYS cc_start: 0.8861 (tttt) cc_final: 0.8524 (tppp) REVERT: I 265 TYR cc_start: 0.9193 (t80) cc_final: 0.8876 (t80) REVERT: I 301 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8211 (mm-30) REVERT: I 317 LYS cc_start: 0.8865 (pptt) cc_final: 0.8639 (pptt) outliers start: 51 outliers final: 35 residues processed: 332 average time/residue: 0.2053 time to fit residues: 97.7162 Evaluate side-chains 324 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 274 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 281 optimal weight: 9.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 340 GLN I 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089267 restraints weight = 54918.297| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.67 r_work: 0.3119 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24272 Z= 0.133 Angle : 0.593 15.346 33150 Z= 0.306 Chirality : 0.040 0.203 3627 Planarity : 0.004 0.044 4215 Dihedral : 13.946 149.848 4178 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.98 % Allowed : 15.04 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 2946 helix: 0.61 (0.18), residues: 865 sheet: 0.13 (0.25), residues: 441 loop : -2.03 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 184 TYR 0.022 0.002 TYR B 235 PHE 0.010 0.001 PHE I 322 TRP 0.032 0.001 TRP B 414 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00297 (24272) covalent geometry : angle 0.59278 (33150) hydrogen bonds : bond 0.03044 ( 772) hydrogen bonds : angle 4.56983 ( 2209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 0.897 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: A 13 THR cc_start: 0.9111 (p) cc_final: 0.8896 (p) REVERT: A 16 GLN cc_start: 0.8549 (mp10) cc_final: 0.8332 (mm-40) REVERT: A 19 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8579 (tm-30) REVERT: A 26 SER cc_start: 0.8080 (t) cc_final: 0.7598 (p) REVERT: A 37 TYR cc_start: 0.9013 (t80) cc_final: 0.8742 (t80) REVERT: A 38 TYR cc_start: 0.9268 (t80) cc_final: 0.8878 (t80) REVERT: A 41 ASP cc_start: 0.9075 (t70) cc_final: 0.8254 (t0) REVERT: B 74 HIS cc_start: 0.9113 (t-90) cc_final: 0.8880 (t70) REVERT: B 82 LEU cc_start: 0.9163 (mt) cc_final: 0.8783 (mt) REVERT: B 104 LEU cc_start: 0.9392 (tt) cc_final: 0.8993 (mp) REVERT: B 118 PHE cc_start: 0.8903 (t80) cc_final: 0.8566 (t80) REVERT: B 133 TRP cc_start: 0.7665 (m-90) cc_final: 0.7242 (m-10) REVERT: B 208 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8578 (tm-30) REVERT: B 220 GLU cc_start: 0.9144 (tt0) cc_final: 0.8626 (tp30) REVERT: B 242 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8730 (tppt) REVERT: B 308 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.5646 (pp) REVERT: B 319 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8350 (mpt180) REVERT: B 332 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9031 (tm-30) REVERT: B 423 THR cc_start: 0.8820 (m) cc_final: 0.8342 (p) REVERT: B 424 MET cc_start: 0.8739 (ppp) cc_final: 0.8359 (ppp) REVERT: B 427 GLU cc_start: 0.9344 (mp0) cc_final: 0.9124 (mp0) REVERT: C 50 ILE cc_start: 0.9216 (pt) cc_final: 0.8987 (mm) REVERT: C 77 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7422 (mmm160) REVERT: C 149 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6716 (t160) REVERT: C 170 ARG cc_start: 0.9107 (ttp-110) cc_final: 0.8824 (ttp-110) REVERT: C 198 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8798 (pp20) REVERT: C 262 TYR cc_start: 0.8538 (m-80) cc_final: 0.8169 (m-80) REVERT: D 40 ASP cc_start: 0.8385 (m-30) cc_final: 0.8116 (m-30) REVERT: D 63 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7824 (ptm160) REVERT: D 301 GLU cc_start: 0.8850 (pt0) cc_final: 0.8446 (mp0) REVERT: D 328 ASN cc_start: 0.8508 (m-40) cc_final: 0.8293 (p0) REVERT: E 33 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8452 (mm-30) REVERT: E 64 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7605 (tp30) REVERT: E 95 GLN cc_start: 0.8501 (mt0) cc_final: 0.7955 (pt0) REVERT: E 138 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8501 (mm-40) REVERT: E 184 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7106 (mtp85) REVERT: F 64 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8444 (tt0) REVERT: F 78 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8075 (ttpp) REVERT: F 86 ASP cc_start: 0.8832 (m-30) cc_final: 0.8086 (t0) REVERT: F 98 ASP cc_start: 0.8428 (m-30) cc_final: 0.7997 (m-30) REVERT: F 260 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8367 (ttmm) REVERT: F 268 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8500 (mtm-85) REVERT: F 269 ASP cc_start: 0.8697 (m-30) cc_final: 0.8067 (t0) REVERT: G 90 GLN cc_start: 0.8789 (mt0) cc_final: 0.8226 (mp10) REVERT: G 95 GLN cc_start: 0.8753 (mt0) cc_final: 0.8491 (mt0) REVERT: G 135 LYS cc_start: 0.9353 (tppt) cc_final: 0.9060 (tptm) REVERT: G 215 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8197 (mp0) REVERT: H 28 SER cc_start: 0.9499 (m) cc_final: 0.9117 (t) REVERT: H 51 ARG cc_start: 0.4644 (mmt-90) cc_final: 0.1053 (mtt-85) REVERT: H 84 LYS cc_start: 0.8921 (mttp) cc_final: 0.8648 (ptpp) REVERT: H 138 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8367 (mm-40) REVERT: H 226 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6757 (t-90) REVERT: H 333 ASP cc_start: 0.8917 (t0) cc_final: 0.8693 (t0) REVERT: I 64 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8051 (mp0) REVERT: I 67 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9116 (m) REVERT: I 84 LYS cc_start: 0.8837 (pttp) cc_final: 0.8602 (pttp) REVERT: I 145 ASN cc_start: 0.8835 (m-40) cc_final: 0.8571 (m110) REVERT: I 146 ASP cc_start: 0.8641 (t0) cc_final: 0.8416 (m-30) REVERT: I 202 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8059 (ttt180) REVERT: I 211 ASP cc_start: 0.8919 (m-30) cc_final: 0.8581 (m-30) REVERT: I 255 ASP cc_start: 0.8452 (t70) cc_final: 0.7951 (p0) REVERT: I 260 LYS cc_start: 0.8822 (tttt) cc_final: 0.8493 (tppp) REVERT: I 301 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8186 (mm-30) REVERT: I 334 GLU cc_start: 0.8774 (tp30) cc_final: 0.8465 (tm-30) outliers start: 44 outliers final: 29 residues processed: 327 average time/residue: 0.2104 time to fit residues: 98.3494 Evaluate side-chains 318 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 230 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 292 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089855 restraints weight = 54781.827| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.69 r_work: 0.3135 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24272 Z= 0.123 Angle : 0.597 13.729 33150 Z= 0.305 Chirality : 0.040 0.208 3627 Planarity : 0.004 0.047 4215 Dihedral : 13.888 150.326 4178 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.66 % Allowed : 15.54 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 2946 helix: 0.64 (0.18), residues: 865 sheet: 0.25 (0.25), residues: 438 loop : -1.99 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 184 TYR 0.025 0.002 TYR E 156 PHE 0.010 0.001 PHE D 165 TRP 0.060 0.002 TRP D 57 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00277 (24272) covalent geometry : angle 0.59724 (33150) hydrogen bonds : bond 0.02966 ( 772) hydrogen bonds : angle 4.51153 ( 2209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.865 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: A 13 THR cc_start: 0.9134 (p) cc_final: 0.8819 (t) REVERT: A 16 GLN cc_start: 0.8564 (mp10) cc_final: 0.8342 (mm-40) REVERT: A 19 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8525 (tm-30) REVERT: A 26 SER cc_start: 0.8053 (t) cc_final: 0.7583 (p) REVERT: A 37 TYR cc_start: 0.8997 (t80) cc_final: 0.8754 (t80) REVERT: A 38 TYR cc_start: 0.9266 (t80) cc_final: 0.8913 (t80) REVERT: A 41 ASP cc_start: 0.9064 (t70) cc_final: 0.8220 (t0) REVERT: A 77 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7981 (tpp80) REVERT: B 74 HIS cc_start: 0.9088 (t-90) cc_final: 0.8878 (t70) REVERT: B 82 LEU cc_start: 0.9142 (mt) cc_final: 0.8842 (mt) REVERT: B 118 PHE cc_start: 0.8906 (t80) cc_final: 0.8596 (t80) REVERT: B 133 TRP cc_start: 0.7641 (m-90) cc_final: 0.7236 (m-10) REVERT: B 220 GLU cc_start: 0.9108 (tt0) cc_final: 0.8587 (tp30) REVERT: B 263 TRP cc_start: 0.8785 (m100) cc_final: 0.8541 (m100) REVERT: B 308 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.5692 (pp) REVERT: B 319 ARG cc_start: 0.8731 (mmp80) cc_final: 0.8342 (mpt180) REVERT: B 332 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8987 (tm-30) REVERT: B 424 MET cc_start: 0.8745 (ppp) cc_final: 0.8399 (ppp) REVERT: C 50 ILE cc_start: 0.9187 (pt) cc_final: 0.8962 (mm) REVERT: C 77 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7200 (tpt90) REVERT: C 85 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8208 (tpp80) REVERT: C 170 ARG cc_start: 0.9096 (ttp-110) cc_final: 0.8773 (ttp-110) REVERT: C 198 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8788 (pp20) REVERT: C 262 TYR cc_start: 0.8450 (m-80) cc_final: 0.8114 (m-80) REVERT: D 63 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7868 (ptm160) REVERT: D 301 GLU cc_start: 0.8815 (pt0) cc_final: 0.8421 (mp0) REVERT: E 33 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8471 (mm-30) REVERT: E 64 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7619 (tp30) REVERT: E 95 GLN cc_start: 0.8524 (mt0) cc_final: 0.7969 (pt0) REVERT: E 138 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8482 (mm-40) REVERT: E 184 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7061 (mtp85) REVERT: E 311 LYS cc_start: 0.8660 (ptmm) cc_final: 0.8256 (ptmm) REVERT: F 64 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8473 (tt0) REVERT: F 78 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8530 (ptpp) REVERT: F 86 ASP cc_start: 0.8738 (m-30) cc_final: 0.8053 (t0) REVERT: F 98 ASP cc_start: 0.8443 (m-30) cc_final: 0.7993 (m-30) REVERT: F 260 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8365 (ttmm) REVERT: F 268 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: F 269 ASP cc_start: 0.8706 (m-30) cc_final: 0.8080 (t0) REVERT: G 33 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8656 (mt-10) REVERT: G 90 GLN cc_start: 0.8777 (mt0) cc_final: 0.8210 (mp10) REVERT: G 95 GLN cc_start: 0.8755 (mt0) cc_final: 0.8545 (mt0) REVERT: G 135 LYS cc_start: 0.9355 (tppt) cc_final: 0.9060 (tptm) REVERT: G 215 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8179 (mp0) REVERT: G 291 ASP cc_start: 0.8394 (p0) cc_final: 0.8172 (p0) REVERT: H 51 ARG cc_start: 0.4594 (mmt-90) cc_final: 0.1069 (mtt-85) REVERT: H 133 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8527 (ttm110) REVERT: H 226 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6630 (t-90) REVERT: H 333 ASP cc_start: 0.8920 (t0) cc_final: 0.8700 (t0) REVERT: I 64 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8060 (mp0) REVERT: I 67 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9106 (m) REVERT: I 84 LYS cc_start: 0.8820 (pttp) cc_final: 0.8587 (pttp) REVERT: I 145 ASN cc_start: 0.8817 (m-40) cc_final: 0.8530 (m110) REVERT: I 146 ASP cc_start: 0.8637 (t0) cc_final: 0.8373 (m-30) REVERT: I 202 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8051 (ttt180) REVERT: I 211 ASP cc_start: 0.8918 (m-30) cc_final: 0.8579 (m-30) REVERT: I 255 ASP cc_start: 0.8485 (t70) cc_final: 0.7957 (p0) REVERT: I 260 LYS cc_start: 0.8816 (tttt) cc_final: 0.8486 (tppp) REVERT: I 268 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8482 (mtp180) REVERT: I 301 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8183 (mm-30) REVERT: I 334 GLU cc_start: 0.8764 (tp30) cc_final: 0.8465 (tm-30) outliers start: 37 outliers final: 25 residues processed: 316 average time/residue: 0.2051 time to fit residues: 93.0914 Evaluate side-chains 314 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 168 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 200 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN F 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087667 restraints weight = 54713.985| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.65 r_work: 0.3088 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24272 Z= 0.180 Angle : 0.632 14.549 33150 Z= 0.325 Chirality : 0.041 0.249 3627 Planarity : 0.004 0.063 4215 Dihedral : 13.936 149.948 4178 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.62 % Allowed : 15.85 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 2946 helix: 0.57 (0.18), residues: 876 sheet: 0.32 (0.25), residues: 436 loop : -2.01 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 184 TYR 0.031 0.002 TYR E 156 PHE 0.013 0.001 PHE B 16 TRP 0.069 0.002 TRP D 57 HIS 0.009 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00398 (24272) covalent geometry : angle 0.63228 (33150) hydrogen bonds : bond 0.03283 ( 772) hydrogen bonds : angle 4.65139 ( 2209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.64 seconds wall clock time: 98 minutes 54.79 seconds (5934.79 seconds total)