Starting phenix.real_space_refine on Sat Feb 7 07:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6t_32335/02_2026/7w6t_32335.map" } resolution = 3.85 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= -0.005 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 178 5.16 5 C 20432 2.51 5 N 5326 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 247 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31768 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "G" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "I" Number of atoms: 6024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6024 Classifications: {'peptide': 749} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 715} Chain breaks: 1 Chain: "J" Number of atoms: 6024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6024 Classifications: {'peptide': 749} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 715} Chain breaks: 1 Time building chain proxies: 6.81, per 1000 atoms: 0.21 Number of scatterers: 31768 At special positions: 0 Unit cell: (199.758, 162.24, 209.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 178 16.00 O 5832 8.00 N 5326 7.00 C 20432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS I 357 " distance=2.03 Simple disulfide: pdb=" SG CYS I 466 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS I 475 " - pdb=" SG CYS I 493 " distance=2.02 Simple disulfide: pdb=" SG CYS I 674 " - pdb=" SG CYS I 785 " distance=2.02 Simple disulfide: pdb=" SG CYS J 350 " - pdb=" SG CYS J 357 " distance=2.02 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS J 469 " distance=2.03 Simple disulfide: pdb=" SG CYS J 475 " - pdb=" SG CYS J 493 " distance=2.02 Simple disulfide: pdb=" SG CYS J 674 " - pdb=" SG CYS J 785 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7448 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 31 sheets defined 51.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.622A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.340A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 removed outlier: 4.037A pdb=" N ASN A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.557A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.624A pdb=" N ARG A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.727A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.958A pdb=" N LYS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 23 Proline residue: B 21 - end of helix No H-bonds generated for 'chain 'B' and resid 18 through 23' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 74 removed outlier: 4.154A pdb=" N PHE B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.211A pdb=" N PHE B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.776A pdb=" N LYS B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 179 through 203 removed outlier: 3.529A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.506A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.986A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 303 removed outlier: 3.606A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.098A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 removed outlier: 3.655A pdb=" N LEU B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.798A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 397 removed outlier: 3.906A pdb=" N LYS B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.684A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 4.228A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.735A pdb=" N ALA C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.925A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.613A pdb=" N PHE C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 removed outlier: 3.805A pdb=" N TYR C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 4.205A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 154 through 170 removed outlier: 4.044A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 170 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 removed outlier: 4.182A pdb=" N VAL C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.698A pdb=" N ALA D 7 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 18 through 23 removed outlier: 4.483A pdb=" N VAL D 22 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.994A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.565A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 292 through 303 removed outlier: 4.188A pdb=" N ARG D 296 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 298 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 4.038A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.825A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 357 through 365 Processing helix chain 'D' and resid 380 through 396 Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.380A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.830A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.567A pdb=" N PHE E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 106 removed outlier: 4.168A pdb=" N TYR E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 131 removed outlier: 3.735A pdb=" N ALA E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.612A pdb=" N MET E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 194 removed outlier: 3.873A pdb=" N VAL E 186 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'F' and resid 8 through 16 removed outlier: 3.865A pdb=" N ALA F 12 " --> pdb=" O TRP F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 69 through 74 removed outlier: 3.945A pdb=" N GLU F 72 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 73 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.828A pdb=" N CYS F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 94 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.512A pdb=" N TYR F 114 " --> pdb=" O CYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.567A pdb=" N ASN F 175 " --> pdb=" O ARG F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 179 through 203 removed outlier: 3.749A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.592A pdb=" N LEU F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 276 removed outlier: 3.528A pdb=" N ILE F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.887A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.806A pdb=" N ASP F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 292 through 303 removed outlier: 4.310A pdb=" N ARG F 296 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 299 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 343 removed outlier: 3.933A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 321 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 366 removed outlier: 4.390A pdb=" N TYR F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 396 Processing helix chain 'F' and resid 397 through 425 removed outlier: 4.400A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.667A pdb=" N LEU F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 486 No H-bonds generated for 'chain 'F' and resid 484 through 486' Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 61 through 75 removed outlier: 4.004A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.891A pdb=" N GLN G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 110 removed outlier: 4.801A pdb=" N TYR G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 105 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 removed outlier: 3.871A pdb=" N ALA G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.936A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 194 removed outlier: 4.155A pdb=" N VAL G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 189 " --> pdb=" O HIS G 185 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS G 192 " --> pdb=" O VAL G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 213 through 221 removed outlier: 3.780A pdb=" N MET G 217 " --> pdb=" O ASP G 213 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 8 through 16 removed outlier: 3.530A pdb=" N ALA H 12 " --> pdb=" O TRP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 89 through 101 removed outlier: 3.565A pdb=" N CYS H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.746A pdb=" N ILE H 128 " --> pdb=" O PRO H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 180 through 203 removed outlier: 3.796A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 Processing helix chain 'H' and resid 257 through 276 removed outlier: 4.291A pdb=" N ILE H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Proline residue: H 269 - end of helix Processing helix chain 'H' and resid 277 through 281 removed outlier: 3.847A pdb=" N ASP H 281 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 293 removed outlier: 3.940A pdb=" N PHE H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL H 287 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 302 removed outlier: 3.613A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.808A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS H 317 " --> pdb=" O THR H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 342 removed outlier: 3.534A pdb=" N LEU H 321 " --> pdb=" O CYS H 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 356 No H-bonds generated for 'chain 'H' and resid 354 through 356' Processing helix chain 'H' and resid 357 through 366 removed outlier: 3.975A pdb=" N THR H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 396 removed outlier: 4.027A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 426 removed outlier: 4.609A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG H 426 " --> pdb=" O GLN H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.889A pdb=" N LEU H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 480 " --> pdb=" O HIS H 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 56 removed outlier: 3.742A pdb=" N LEU I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU I 43 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL I 50 " --> pdb=" O CYS I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 76 Processing helix chain 'I' and resid 77 through 81 Processing helix chain 'I' and resid 119 through 125 removed outlier: 3.591A pdb=" N ILE I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU I 124 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER I 125 " --> pdb=" O LYS I 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 119 through 125' Processing helix chain 'I' and resid 229 through 235 Processing helix chain 'I' and resid 314 through 318 Processing helix chain 'I' and resid 394 through 396 No H-bonds generated for 'chain 'I' and resid 394 through 396' Processing helix chain 'I' and resid 518 through 528 removed outlier: 3.779A pdb=" N ASN I 526 " --> pdb=" O GLN I 522 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP I 527 " --> pdb=" O LYS I 523 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG I 528 " --> pdb=" O ALA I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 590 Processing helix chain 'I' and resid 607 through 613 removed outlier: 4.458A pdb=" N LEU I 611 " --> pdb=" O GLN I 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU I 612 " --> pdb=" O GLY I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 616 No H-bonds generated for 'chain 'I' and resid 614 through 616' Processing helix chain 'I' and resid 620 through 637 removed outlier: 3.846A pdb=" N LYS I 625 " --> pdb=" O PHE I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 652 through 661 Processing helix chain 'I' and resid 683 through 687 Processing helix chain 'I' and resid 688 through 697 removed outlier: 3.851A pdb=" N TYR I 695 " --> pdb=" O PHE I 691 " (cutoff:3.500A) Processing helix chain 'I' and resid 703 through 709 Processing helix chain 'I' and resid 710 through 716 removed outlier: 3.987A pdb=" N ARG I 714 " --> pdb=" O LYS I 710 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER I 716 " --> pdb=" O ALA I 712 " (cutoff:3.500A) Processing helix chain 'I' and resid 736 through 750 removed outlier: 4.320A pdb=" N LEU I 742 " --> pdb=" O HIS I 738 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN I 745 " --> pdb=" O GLU I 741 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 786 removed outlier: 3.725A pdb=" N HIS I 773 " --> pdb=" O ALA I 769 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU I 784 " --> pdb=" O GLY I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 56 removed outlier: 3.545A pdb=" N LEU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 394 through 396 No H-bonds generated for 'chain 'J' and resid 394 through 396' Processing helix chain 'J' and resid 518 through 526 removed outlier: 3.647A pdb=" N ASN J 526 " --> pdb=" O GLN J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 592 removed outlier: 3.563A pdb=" N VAL J 587 " --> pdb=" O THR J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 613 Processing helix chain 'J' and resid 614 through 616 No H-bonds generated for 'chain 'J' and resid 614 through 616' Processing helix chain 'J' and resid 620 through 635 removed outlier: 3.549A pdb=" N GLU J 624 " --> pdb=" O GLY J 620 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS J 625 " --> pdb=" O PHE J 621 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL J 631 " --> pdb=" O GLN J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 661 Processing helix chain 'J' and resid 688 through 696 removed outlier: 4.289A pdb=" N TYR J 695 " --> pdb=" O PHE J 691 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU J 696 " --> pdb=" O SER J 692 " (cutoff:3.500A) Processing helix chain 'J' and resid 703 through 710 removed outlier: 3.821A pdb=" N GLU J 707 " --> pdb=" O ASN J 703 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET J 708 " --> pdb=" O ARG J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 716 removed outlier: 4.586A pdb=" N SER J 716 " --> pdb=" O ALA J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 735 through 738 Processing helix chain 'J' and resid 739 through 750 removed outlier: 3.661A pdb=" N THR J 744 " --> pdb=" O ALA J 740 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN J 745 " --> pdb=" O GLU J 741 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 787 removed outlier: 4.105A pdb=" N GLU J 784 " --> pdb=" O GLY J 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 removed outlier: 3.703A pdb=" N TYR B 82 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 49 through 54 Processing sheet with id=AA4, first strand: chain 'F' and resid 49 through 54 removed outlier: 3.663A pdb=" N TYR F 82 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 154 Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 54 removed outlier: 8.665A pdb=" N TYR H 82 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL H 43 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE H 84 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN H 45 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 88 through 89 removed outlier: 3.563A pdb=" N LYS I 88 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 96 " --> pdb=" O LYS I 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 139 through 147 removed outlier: 3.727A pdb=" N TYR I 157 " --> pdb=" O TYR I 144 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL I 146 " --> pdb=" O THR I 155 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR I 155 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR I 158 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 183 through 186 removed outlier: 4.164A pdb=" N PHE I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'I' and resid 266 through 267 removed outlier: 3.955A pdb=" N LEU I 267 " --> pdb=" O LYS I 279 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 279 " --> pdb=" O LEU I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 295 through 296 removed outlier: 3.868A pdb=" N LEU I 295 " --> pdb=" O MET I 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 320 through 322 removed outlier: 3.541A pdb=" N LEU I 338 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL I 344 " --> pdb=" O ASN I 339 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER I 345 " --> pdb=" O GLU I 362 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU I 362 " --> pdb=" O SER I 345 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU I 347 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 377 through 378 removed outlier: 3.516A pdb=" N ARG I 389 " --> pdb=" O HIS I 401 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 426 through 433 removed outlier: 6.980A pdb=" N TYR I 440 " --> pdb=" O LEU I 430 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR I 432 " --> pdb=" O LYS I 438 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS I 438 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 478 through 480 removed outlier: 6.593A pdb=" N VAL I 501 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU I 515 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN I 505 " --> pdb=" O ARG I 511 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG I 511 " --> pdb=" O ASN I 505 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 532 through 540 removed outlier: 4.285A pdb=" N VAL I 596 " --> pdb=" O LEU I 550 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL I 597 " --> pdb=" O PRO I 562 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU I 564 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR I 561 " --> pdb=" O ASP I 641 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR I 643 " --> pdb=" O TYR I 561 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU I 563 " --> pdb=" O THR I 643 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL I 645 " --> pdb=" O LEU I 563 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU I 565 " --> pdb=" O VAL I 645 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL I 647 " --> pdb=" O LEU I 565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 677 through 678 removed outlier: 5.976A pdb=" N ALA I 677 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE I 725 " --> pdb=" O GLN I 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 94 through 98 removed outlier: 7.327A pdb=" N VAL J 104 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU J 117 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 130 through 132 removed outlier: 4.133A pdb=" N ARG J 130 " --> pdb=" O SER J 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 130 through 132 removed outlier: 4.133A pdb=" N ARG J 130 " --> pdb=" O SER J 143 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY J 156 " --> pdb=" O LEU J 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 183 through 186 removed outlier: 4.174A pdb=" N TYR J 183 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE J 196 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY J 185 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 194 " --> pdb=" O GLY J 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.985A pdb=" N LEU J 295 " --> pdb=" O MET J 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 264 through 267 Processing sheet with id=AC7, first strand: chain 'J' and resid 325 through 326 removed outlier: 4.270A pdb=" N LYS J 326 " --> pdb=" O ALA J 334 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA J 334 " --> pdb=" O LYS J 326 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER J 345 " --> pdb=" O GLU J 362 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU J 362 " --> pdb=" O SER J 345 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU J 347 " --> pdb=" O LYS J 360 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS J 360 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 387 through 392 removed outlier: 3.909A pdb=" N ARG J 389 " --> pdb=" O HIS J 401 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 426 through 431 removed outlier: 7.664A pdb=" N LEU J 442 " --> pdb=" O THR J 427 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE J 429 " --> pdb=" O TYR J 440 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR J 440 " --> pdb=" O ILE J 429 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER J 431 " --> pdb=" O LYS J 438 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LYS J 438 " --> pdb=" O SER J 431 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE J 441 " --> pdb=" O TYR J 454 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER J 443 " --> pdb=" O HIS J 452 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS J 452 " --> pdb=" O SER J 443 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 478 through 482 Processing sheet with id=AD2, first strand: chain 'J' and resid 532 through 539 removed outlier: 3.746A pdb=" N VAL J 595 " --> pdb=" O PRO J 562 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 597 " --> pdb=" O LEU J 564 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR J 561 " --> pdb=" O ASP J 641 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR J 643 " --> pdb=" O TYR J 561 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU J 563 " --> pdb=" O THR J 643 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL J 645 " --> pdb=" O LEU J 563 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU J 565 " --> pdb=" O VAL J 645 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL J 647 " --> pdb=" O LEU J 565 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 674 through 675 Processing sheet with id=AD4, first strand: chain 'J' and resid 725 through 728 1357 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 3.96 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: 7874 1.33 - 1.45: 6800 1.45 - 1.57: 17590 1.57 - 1.69: 0 1.69 - 1.81: 278 Bond restraints: 32542 Sorted by residual: bond pdb=" CA LYS D 350 " pdb=" C LYS D 350 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.37e-02 5.33e+03 1.68e+01 bond pdb=" CA LYS F 350 " pdb=" C LYS F 350 " ideal model delta sigma weight residual 1.522 1.461 0.061 1.72e-02 3.38e+03 1.26e+01 bond pdb=" CA ASN B 45 " pdb=" CB ASN B 45 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C PHE I 95 " pdb=" N ILE I 96 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.14e-02 7.69e+03 8.41e+00 bond pdb=" CA LYS B 350 " pdb=" C LYS B 350 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.39e-02 5.18e+03 6.27e+00 ... (remaining 32537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 42791 2.18 - 4.35: 1143 4.35 - 6.53: 104 6.53 - 8.70: 26 8.70 - 10.88: 4 Bond angle restraints: 44068 Sorted by residual: angle pdb=" C PRO I 284 " pdb=" N LYS I 285 " pdb=" CA LYS I 285 " ideal model delta sigma weight residual 122.77 114.78 7.99 1.33e+00 5.65e-01 3.61e+01 angle pdb=" C GLY J 495 " pdb=" N PRO J 496 " pdb=" CD PRO J 496 " ideal model delta sigma weight residual 120.60 109.99 10.61 2.20e+00 2.07e-01 2.33e+01 angle pdb=" C GLY J 495 " pdb=" N PRO J 496 " pdb=" CA PRO J 496 " ideal model delta sigma weight residual 127.00 137.88 -10.88 2.40e+00 1.74e-01 2.05e+01 angle pdb=" N TYR I 652 " pdb=" CA TYR I 652 " pdb=" C TYR I 652 " ideal model delta sigma weight residual 114.62 109.67 4.95 1.14e+00 7.69e-01 1.89e+01 angle pdb=" C HIS I 560 " pdb=" N TYR I 561 " pdb=" CA TYR I 561 " ideal model delta sigma weight residual 122.74 112.41 10.33 2.44e+00 1.68e-01 1.79e+01 ... (remaining 44063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17173 17.77 - 35.54: 1856 35.54 - 53.31: 281 53.31 - 71.08: 47 71.08 - 88.85: 17 Dihedral angle restraints: 19374 sinusoidal: 7818 harmonic: 11556 Sorted by residual: dihedral pdb=" CA LEU I 267 " pdb=" C LEU I 267 " pdb=" N PRO I 268 " pdb=" CA PRO I 268 " ideal model delta harmonic sigma weight residual -180.00 -144.26 -35.74 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA GLY G 78 " pdb=" C GLY G 78 " pdb=" N VAL G 79 " pdb=" CA VAL G 79 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ASP I 760 " pdb=" C ASP I 760 " pdb=" N GLU I 761 " pdb=" CA GLU I 761 " ideal model delta harmonic sigma weight residual 180.00 147.35 32.65 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 19371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3007 0.039 - 0.077: 1389 0.077 - 0.116: 376 0.116 - 0.154: 75 0.154 - 0.193: 9 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CB VAL D 401 " pdb=" CA VAL D 401 " pdb=" CG1 VAL D 401 " pdb=" CG2 VAL D 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CB VAL J 567 " pdb=" CA VAL J 567 " pdb=" CG1 VAL J 567 " pdb=" CG2 VAL J 567 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CG LEU J 307 " pdb=" CB LEU J 307 " pdb=" CD1 LEU J 307 " pdb=" CD2 LEU J 307 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 4853 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 477 " -0.031 2.00e-02 2.50e+03 2.18e-02 9.54e+00 pdb=" CG TYR J 477 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR J 477 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 477 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 477 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 477 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 477 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN J 290 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO J 291 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO J 291 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 291 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 354 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO F 355 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " 0.040 5.00e-02 4.00e+02 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 739 2.61 - 3.18: 32719 3.18 - 3.75: 54629 3.75 - 4.33: 76093 4.33 - 4.90: 114062 Nonbonded interactions: 278242 Sorted by model distance: nonbonded pdb=" OH TYR B 370 " pdb=" OG1 THR D 364 " model vdw 2.034 3.040 nonbonded pdb=" OG1 THR H 64 " pdb=" OH TYR H 98 " model vdw 2.040 3.040 nonbonded pdb=" O LYS J 285 " pdb=" OG SER J 689 " model vdw 2.063 3.040 nonbonded pdb=" OH TYR I 150 " pdb=" OH TYR I 224 " model vdw 2.084 3.040 nonbonded pdb=" O HIS D 104 " pdb=" OH TYR D 114 " model vdw 2.085 3.040 ... (remaining 278237 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.790 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 : 0.006 0.064 32550 Z= 0.281 Angle : 0.866 10.876 44084 Z= 0.510 Chirality : 0.046 0.193 4856 Planarity : 0.005 0.072 5610 Dihedral : 14.587 88.852 11902 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 32.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.71 % Favored : 89.24 % Rotamer: Outliers : 0.29 % Allowed : 9.98 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.16 % 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: -4.74 (0.10), residues: 3894 helix: -3.03 (0.09), residues: 1770 sheet: -2.97 (0.26), residues: 303 loop : -3.26 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 449 TYR 0.052 0.002 TYR J 477 PHE 0.028 0.002 PHE I 489 TRP 0.028 0.003 TRP J 230 HIS 0.020 0.002 HIS J 727 Details of bonding type rmsd covalent geometry : bond 0.00580 (32542) covalent geometry : angle 0.86585 (44068) SS BOND : bond 0.00622 ( 8) SS BOND : angle 1.48113 ( 16) hydrogen bonds : bond 0.23427 ( 1348) hydrogen bonds : angle 8.92884 ( 3807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 348 time to evaluate : 1.136 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: symmetry clash REVERT: A 169 MET cc_start: 0.5183 (tpt) cc_final: 0.3854 (ptt) REVERT: B 169 MET cc_start: 0.9026 (ptm) cc_final: 0.8783 (ptp) REVERT: B 235 MET cc_start: 0.9134 (ttp) cc_final: 0.8729 (tmm) REVERT: B 268 MET cc_start: 0.8682 (ppp) cc_final: 0.8390 (ppp) REVERT: B 328 LEU cc_start: 0.9274 (mt) cc_final: 0.8979 (mt) REVERT: B 339 MET cc_start: 0.8477 (mmm) cc_final: 0.8069 (mmm) REVERT: C 158 MET cc_start: 0.4240 (ptm) cc_final: 0.3720 (ptm) REVERT: E 58 ASN cc_start: 0.7782 (t0) cc_final: 0.7575 (t0) REVERT: E 143 ASN cc_start: 0.7185 (m110) cc_final: 0.6800 (t0) REVERT: E 168 MET cc_start: 0.6314 (ptp) cc_final: 0.5692 (ptp) REVERT: E 217 MET cc_start: 0.1700 (tpt) cc_final: 0.1386 (tpp) REVERT: G 97 ASP cc_start: 0.8745 (t0) cc_final: 0.8416 (t0) REVERT: G 217 MET cc_start: 0.7596 (mpp) cc_final: 0.6975 (mpp) REVERT: I 650 LYS cc_start: 0.6685 (pptt) cc_final: 0.6276 (pptt) REVERT: I 761 GLU cc_start: 0.6858 (tp30) cc_final: 0.6563 (tp30) REVERT: I 766 HIS cc_start: 0.6187 (p-80) cc_final: 0.5845 (m90) REVERT: J 317 MET cc_start: 0.2830 (mmp) cc_final: 0.2054 (mmp) REVERT: J 525 ILE cc_start: 0.8492 (pt) cc_final: 0.8270 (pt) REVERT: J 547 MET cc_start: 0.6271 (tmm) cc_final: 0.5791 (tmm) REVERT: J 595 VAL cc_start: 0.7627 (t) cc_final: 0.6915 (t) REVERT: J 626 ASP cc_start: 0.7252 (m-30) cc_final: 0.6945 (t0) REVERT: J 652 TYR cc_start: 0.7092 (t80) cc_final: 0.5969 (t80) REVERT: J 722 GLN cc_start: 0.8261 (mt0) cc_final: 0.7935 (tm-30) REVERT: J 743 ILE cc_start: 0.5468 (tt) cc_final: 0.5199 (tp) outliers start: 10 outliers final: 3 residues processed: 358 average time/residue: 0.1959 time to fit residues: 112.6330 Evaluate side-chains 254 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain J residue 290 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 405 ASN C 185 HIS D 177 HIS D 422 GLN D 477 HIS E 191 GLN E 211 GLN F 96 ASN F 177 HIS F 405 ASN G 58 ASN G 191 GLN H 177 HIS I 112 ASN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN ** I 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 474 ASN I 484 HIS I 613 GLN I 670 GLN I 713 HIS J 154 HIS J 165 HIS ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 301 ASN J 361 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 437 ASN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 522 GLN J 526 ASN J 613 GLN ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 763 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.105819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087485 restraints weight = 238027.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087369 restraints weight = 157308.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.087409 restraints weight = 125063.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.087719 restraints weight = 119031.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.087906 restraints weight = 105018.800| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32550 Z= 0.209 Angle : 0.761 9.142 44084 Z= 0.401 Chirality : 0.047 0.239 4856 Planarity : 0.006 0.074 5610 Dihedral : 6.227 52.423 4329 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.21 % Allowed : 16.10 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.45 (0.12), residues: 3894 helix: -1.74 (0.11), residues: 1857 sheet: -2.48 (0.25), residues: 346 loop : -2.81 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 415 TYR 0.038 0.002 TYR J 477 PHE 0.038 0.002 PHE J 197 TRP 0.022 0.002 TRP I 245 HIS 0.011 0.002 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00467 (32542) covalent geometry : angle 0.76092 (44068) SS BOND : bond 0.00699 ( 8) SS BOND : angle 1.49988 ( 16) hydrogen bonds : bond 0.05611 ( 1348) hydrogen bonds : angle 6.55066 ( 3807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 297 time to evaluate : 1.119 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: B 235 MET cc_start: 0.8972 (ttp) cc_final: 0.8452 (ppp) REVERT: B 328 LEU cc_start: 0.9120 (mt) cc_final: 0.8854 (mt) REVERT: B 365 MET cc_start: 0.8839 (mtp) cc_final: 0.8572 (mtm) REVERT: D 276 MET cc_start: 0.8512 (mmt) cc_final: 0.8311 (mmm) REVERT: E 168 MET cc_start: 0.6125 (ptp) cc_final: 0.5437 (ptp) REVERT: E 220 LEU cc_start: 0.2346 (tp) cc_final: 0.1886 (tp) REVERT: G 89 TYR cc_start: 0.8881 (t80) cc_final: 0.8672 (t80) REVERT: G 97 ASP cc_start: 0.8694 (t0) cc_final: 0.8472 (t0) REVERT: G 217 MET cc_start: 0.7379 (mpp) cc_final: 0.6592 (mpp) REVERT: H 259 MET cc_start: 0.8032 (mmt) cc_final: 0.7346 (mmm) REVERT: H 276 MET cc_start: 0.7055 (tpt) cc_final: 0.6854 (tpp) REVERT: I 84 ASP cc_start: -0.1480 (OUTLIER) cc_final: -0.1976 (p0) REVERT: I 154 HIS cc_start: 0.7464 (p-80) cc_final: 0.7235 (p-80) REVERT: I 175 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5810 (pt0) REVERT: I 220 GLU cc_start: 0.5140 (OUTLIER) cc_final: 0.4584 (pm20) REVERT: I 327 TRP cc_start: -0.0434 (m100) cc_final: -0.0697 (m100) REVERT: I 454 TYR cc_start: 0.7363 (m-80) cc_final: 0.7161 (m-80) REVERT: I 486 MET cc_start: -0.2133 (mpp) cc_final: -0.2464 (mpp) REVERT: I 600 ASP cc_start: 0.0647 (OUTLIER) cc_final: 0.0355 (t0) REVERT: I 650 LYS cc_start: 0.6438 (pptt) cc_final: 0.6080 (pptt) REVERT: J 317 MET cc_start: 0.2911 (mmp) cc_final: 0.2412 (mmp) REVERT: J 324 MET cc_start: -0.0828 (tmm) cc_final: -0.1243 (mmm) REVERT: J 652 TYR cc_start: 0.6689 (t80) cc_final: 0.6052 (t80) REVERT: J 722 GLN cc_start: 0.7940 (mt0) cc_final: 0.7593 (tm-30) REVERT: J 732 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7487 (mm-30) outliers start: 77 outliers final: 37 residues processed: 356 average time/residue: 0.1693 time to fit residues: 101.3536 Evaluate side-chains 296 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 629 GLU Chi-restraints excluded: chain J residue 744 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 204 optimal weight: 9.9990 chunk 43 optimal weight: 0.2980 chunk 324 optimal weight: 5.9990 chunk 187 optimal weight: 40.0000 chunk 170 optimal weight: 0.0270 chunk 206 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 276 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 overall best weight: 2.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 221 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 745 GLN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** 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 = 0.4491 r_free = 0.4491 target = 0.106757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.090196 restraints weight = 237276.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.089476 restraints weight = 133829.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.089745 restraints weight = 106845.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.089847 restraints weight = 95606.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.089921 restraints weight = 90037.507| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32550 Z= 0.157 Angle : 0.686 12.621 44084 Z= 0.358 Chirality : 0.045 0.177 4856 Planarity : 0.005 0.055 5610 Dihedral : 5.795 53.946 4327 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.70 % Allowed : 18.20 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.77 (0.12), residues: 3894 helix: -1.17 (0.11), residues: 1861 sheet: -2.26 (0.25), residues: 379 loop : -2.44 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 776 TYR 0.035 0.002 TYR D 312 PHE 0.033 0.002 PHE J 197 TRP 0.018 0.002 TRP J 327 HIS 0.013 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00348 (32542) covalent geometry : angle 0.68558 (44068) SS BOND : bond 0.00511 ( 8) SS BOND : angle 1.07978 ( 16) hydrogen bonds : bond 0.04803 ( 1348) hydrogen bonds : angle 6.02560 ( 3807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 298 time to evaluate : 1.200 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: B 235 MET cc_start: 0.8858 (ttp) cc_final: 0.8575 (ppp) REVERT: B 328 LEU cc_start: 0.9035 (mt) cc_final: 0.8821 (mt) REVERT: C 145 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6281 (t80) REVERT: D 169 MET cc_start: 0.8430 (ptt) cc_final: 0.8203 (ptt) REVERT: E 168 MET cc_start: 0.5769 (ptp) cc_final: 0.5511 (ptp) REVERT: E 220 LEU cc_start: 0.2155 (tp) cc_final: 0.1746 (mp) REVERT: F 1 MET cc_start: 0.5136 (mtt) cc_final: 0.4700 (mtt) REVERT: G 97 ASP cc_start: 0.8279 (t0) cc_final: 0.8077 (t0) REVERT: G 217 MET cc_start: 0.7084 (mpp) cc_final: 0.6450 (mpp) REVERT: H 169 MET cc_start: 0.7576 (ptt) cc_final: 0.7306 (ptt) REVERT: I 175 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5765 (pt0) REVERT: I 265 MET cc_start: 0.5324 (tpt) cc_final: 0.4777 (tpt) REVERT: I 486 MET cc_start: -0.2190 (mpp) cc_final: -0.4494 (mtt) REVERT: I 650 LYS cc_start: 0.6422 (pptt) cc_final: 0.6162 (pptt) REVERT: J 224 TYR cc_start: 0.7563 (m-80) cc_final: 0.7121 (m-80) REVERT: J 235 GLU cc_start: 0.6559 (mm-30) cc_final: 0.5755 (mm-30) REVERT: J 317 MET cc_start: 0.1783 (mmp) cc_final: -0.1514 (tpp) REVERT: J 324 MET cc_start: -0.0892 (tmm) cc_final: -0.1454 (mmm) REVERT: J 530 MET cc_start: 0.8293 (mpp) cc_final: 0.8021 (mpp) REVERT: J 592 HIS cc_start: 0.8172 (m-70) cc_final: 0.7954 (m-70) REVERT: J 628 MET cc_start: 0.5727 (mtt) cc_final: 0.5245 (mmm) REVERT: J 652 TYR cc_start: 0.6346 (t80) cc_final: 0.6106 (t80) REVERT: J 660 ILE cc_start: 0.9344 (mt) cc_final: 0.9070 (mp) REVERT: J 733 LYS cc_start: 0.7851 (tttt) cc_final: 0.7269 (tptm) REVERT: J 741 GLU cc_start: 0.2122 (mm-30) cc_final: 0.1713 (mm-30) outliers start: 94 outliers final: 35 residues processed: 371 average time/residue: 0.1664 time to fit residues: 104.5032 Evaluate side-chains 289 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 301 ASN Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 190 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 249 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 HIS ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** 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 = 0.4463 r_free = 0.4463 target = 0.105518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.088565 restraints weight = 235548.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.087526 restraints weight = 140162.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.087823 restraints weight = 117523.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.088002 restraints weight = 97804.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.088071 restraints weight = 91269.955| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32550 Z= 0.199 Angle : 0.710 10.162 44084 Z= 0.371 Chirality : 0.046 0.256 4856 Planarity : 0.005 0.054 5610 Dihedral : 5.768 59.643 4326 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.42 % Allowed : 19.29 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.51 (0.13), residues: 3894 helix: -0.92 (0.12), residues: 1833 sheet: -2.13 (0.25), residues: 367 loop : -2.34 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 415 TYR 0.029 0.002 TYR J 477 PHE 0.031 0.002 PHE J 197 TRP 0.023 0.002 TRP I 245 HIS 0.012 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00443 (32542) covalent geometry : angle 0.71000 (44068) SS BOND : bond 0.00654 ( 8) SS BOND : angle 1.20165 ( 16) hydrogen bonds : bond 0.04608 ( 1348) hydrogen bonds : angle 5.91684 ( 3807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 256 time to evaluate : 1.138 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: A 193 MET cc_start: 0.4250 (mmm) cc_final: 0.3575 (mmp) REVERT: B 235 MET cc_start: 0.8729 (ttp) cc_final: 0.8484 (ppp) REVERT: B 289 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 328 LEU cc_start: 0.8936 (mt) cc_final: 0.8692 (mt) REVERT: D 276 MET cc_start: 0.8585 (mmm) cc_final: 0.8360 (mmm) REVERT: E 160 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7521 (t70) REVERT: G 101 TYR cc_start: 0.9124 (t80) cc_final: 0.8888 (t80) REVERT: G 217 MET cc_start: 0.7228 (mpp) cc_final: 0.6680 (mpp) REVERT: H 1 MET cc_start: 0.5412 (mpp) cc_final: 0.5008 (mpp) REVERT: I 175 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5766 (pt0) REVERT: I 486 MET cc_start: -0.1849 (mpp) cc_final: -0.2848 (mmt) REVERT: I 650 LYS cc_start: 0.6527 (pptt) cc_final: 0.6217 (pptt) REVERT: J 317 MET cc_start: 0.1742 (mmp) cc_final: -0.1078 (tpp) REVERT: J 530 MET cc_start: 0.8254 (mpp) cc_final: 0.8041 (mpp) REVERT: J 578 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6009 (pm20) REVERT: J 592 HIS cc_start: 0.8160 (m-70) cc_final: 0.7938 (m-70) REVERT: J 628 MET cc_start: 0.5782 (mtt) cc_final: 0.5377 (mmt) REVERT: J 660 ILE cc_start: 0.9353 (mt) cc_final: 0.9016 (mp) REVERT: J 733 LYS cc_start: 0.7899 (tttt) cc_final: 0.7425 (tptm) REVERT: J 767 SER cc_start: 0.8435 (m) cc_final: 0.7966 (t) outliers start: 119 outliers final: 72 residues processed: 356 average time/residue: 0.1596 time to fit residues: 96.0992 Evaluate side-chains 317 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 234 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 118 optimal weight: 50.0000 chunk 386 optimal weight: 10.0000 chunk 163 optimal weight: 40.0000 chunk 290 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 184 GLN E 143 ASN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 ASN ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.105524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.089352 restraints weight = 236904.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.088315 restraints weight = 140757.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.088487 restraints weight = 127649.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.088631 restraints weight = 105333.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.088763 restraints weight = 93712.957| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32550 Z= 0.205 Angle : 0.726 14.403 44084 Z= 0.376 Chirality : 0.046 0.267 4856 Planarity : 0.005 0.057 5610 Dihedral : 5.779 56.699 4326 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.31 % Allowed : 19.67 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -2.29 (0.13), residues: 3894 helix: -0.76 (0.12), residues: 1812 sheet: -2.02 (0.26), residues: 355 loop : -2.20 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 146 TYR 0.027 0.002 TYR G 89 PHE 0.060 0.002 PHE H 383 TRP 0.022 0.002 TRP I 245 HIS 0.013 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00459 (32542) covalent geometry : angle 0.72557 (44068) SS BOND : bond 0.00661 ( 8) SS BOND : angle 1.24735 ( 16) hydrogen bonds : bond 0.04492 ( 1348) hydrogen bonds : angle 5.90049 ( 3807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 257 time to evaluate : 1.154 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 169 MET cc_start: 0.5066 (tpt) cc_final: 0.4660 (mmt) REVERT: D 169 MET cc_start: 0.7700 (ptt) cc_final: 0.7482 (ptt) REVERT: E 59 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5797 (t80) REVERT: E 160 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7708 (t70) REVERT: E 220 LEU cc_start: 0.2508 (tp) cc_final: 0.2012 (mt) REVERT: G 158 MET cc_start: 0.6702 (pmm) cc_final: 0.6429 (pmm) REVERT: G 183 ARG cc_start: 0.9480 (mmm-85) cc_final: 0.9211 (tpp-160) REVERT: G 217 MET cc_start: 0.7397 (mpp) cc_final: 0.6725 (mpp) REVERT: H 1 MET cc_start: 0.4976 (mpp) cc_final: 0.3868 (mpp) REVERT: H 169 MET cc_start: 0.7249 (ptt) cc_final: 0.6961 (ptt) REVERT: I 175 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5551 (pt0) REVERT: I 486 MET cc_start: -0.1595 (mpp) cc_final: -0.2616 (mmt) REVERT: I 782 PHE cc_start: 0.5455 (OUTLIER) cc_final: 0.4269 (m-80) REVERT: J 224 TYR cc_start: 0.7102 (m-80) cc_final: 0.6247 (m-80) REVERT: J 317 MET cc_start: 0.1625 (mmp) cc_final: -0.0778 (tpp) REVERT: J 538 ILE cc_start: 0.8584 (mm) cc_final: 0.8304 (mp) REVERT: J 592 HIS cc_start: 0.8153 (m-70) cc_final: 0.7922 (m-70) REVERT: J 628 MET cc_start: 0.5673 (mtt) cc_final: 0.5386 (mmt) REVERT: J 660 ILE cc_start: 0.9241 (mt) cc_final: 0.8856 (mp) REVERT: J 767 SER cc_start: 0.8524 (m) cc_final: 0.8050 (t) outliers start: 150 outliers final: 93 residues processed: 384 average time/residue: 0.1698 time to fit residues: 110.5887 Evaluate side-chains 337 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 240 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 782 PHE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 265 MET Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 744 THR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 16 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 17 optimal weight: 40.0000 chunk 367 optimal weight: 3.9990 chunk 337 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS I 408 GLN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** 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 = 0.4482 r_free = 0.4482 target = 0.105580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.089481 restraints weight = 235819.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.088397 restraints weight = 145633.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.088889 restraints weight = 115270.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.088886 restraints weight = 98205.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.088935 restraints weight = 96684.770| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32550 Z= 0.189 Angle : 0.721 14.580 44084 Z= 0.370 Chirality : 0.046 0.232 4856 Planarity : 0.005 0.059 5610 Dihedral : 5.682 55.658 4326 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.51 % Allowed : 21.19 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -2.17 (0.13), residues: 3894 helix: -0.68 (0.12), residues: 1838 sheet: -1.93 (0.25), residues: 367 loop : -2.13 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 183 TYR 0.026 0.002 TYR C 104 PHE 0.050 0.002 PHE H 383 TRP 0.020 0.002 TRP I 245 HIS 0.014 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00427 (32542) covalent geometry : angle 0.72055 (44068) SS BOND : bond 0.00635 ( 8) SS BOND : angle 1.15431 ( 16) hydrogen bonds : bond 0.04325 ( 1348) hydrogen bonds : angle 5.85151 ( 3807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 257 time to evaluate : 1.233 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 158 MET cc_start: -0.1698 (OUTLIER) cc_final: -0.2057 (pmm) REVERT: A 193 MET cc_start: 0.3702 (mmm) cc_final: 0.3079 (mmp) REVERT: C 145 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: D 128 ILE cc_start: 0.8215 (mt) cc_final: 0.8010 (mt) REVERT: D 169 MET cc_start: 0.7728 (ptt) cc_final: 0.7525 (ptt) REVERT: E 59 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6292 (t80) REVERT: E 160 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7918 (t70) REVERT: E 220 LEU cc_start: 0.2646 (tp) cc_final: 0.2159 (mt) REVERT: G 158 MET cc_start: 0.6925 (pmm) cc_final: 0.6658 (pmm) REVERT: G 183 ARG cc_start: 0.9477 (mmm-85) cc_final: 0.9114 (tpm170) REVERT: H 393 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (mp) REVERT: I 175 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5599 (pt0) REVERT: I 486 MET cc_start: -0.1323 (mpp) cc_final: -0.2269 (mmt) REVERT: J 105 ILE cc_start: 0.5394 (OUTLIER) cc_final: 0.4927 (mm) REVERT: J 235 GLU cc_start: 0.6580 (mm-30) cc_final: 0.5808 (mm-30) REVERT: J 317 MET cc_start: 0.1483 (mmp) cc_final: -0.0929 (tpp) REVERT: J 523 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: J 538 ILE cc_start: 0.8687 (mm) cc_final: 0.8463 (mp) REVERT: J 578 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: J 592 HIS cc_start: 0.8128 (m-70) cc_final: 0.7880 (m-70) REVERT: J 628 MET cc_start: 0.5945 (mtt) cc_final: 0.5638 (mmt) REVERT: J 660 ILE cc_start: 0.9241 (mt) cc_final: 0.8980 (mp) REVERT: J 664 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7874 (tmtt) REVERT: J 722 GLN cc_start: 0.8037 (mt0) cc_final: 0.7792 (tm-30) REVERT: J 767 SER cc_start: 0.8521 (m) cc_final: 0.8048 (t) outliers start: 122 outliers final: 82 residues processed: 361 average time/residue: 0.1818 time to fit residues: 110.2651 Evaluate side-chains 336 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 245 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 523 LYS Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 87 optimal weight: 20.0000 chunk 333 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 185 optimal weight: 30.0000 chunk 203 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS F 96 ASN I 613 GLN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 627 GLN ** J 703 ASN ** 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 = 0.4496 r_free = 0.4496 target = 0.106412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.090417 restraints weight = 239935.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.089837 restraints weight = 131648.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.090332 restraints weight = 103167.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.090310 restraints weight = 93097.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.090384 restraints weight = 88363.481| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32550 Z= 0.152 Angle : 0.696 13.920 44084 Z= 0.353 Chirality : 0.045 0.273 4856 Planarity : 0.005 0.094 5610 Dihedral : 5.522 55.354 4326 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.42 % Allowed : 22.05 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.97 (0.13), residues: 3894 helix: -0.56 (0.12), residues: 1838 sheet: -1.78 (0.26), residues: 378 loop : -1.97 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 383 TYR 0.022 0.002 TYR C 104 PHE 0.028 0.002 PHE J 197 TRP 0.020 0.002 TRP I 245 HIS 0.014 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00344 (32542) covalent geometry : angle 0.69570 (44068) SS BOND : bond 0.00478 ( 8) SS BOND : angle 0.98593 ( 16) hydrogen bonds : bond 0.04141 ( 1348) hydrogen bonds : angle 5.68316 ( 3807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 263 time to evaluate : 1.257 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 158 MET cc_start: -0.1752 (OUTLIER) cc_final: -0.2103 (pmm) REVERT: A 169 MET cc_start: 0.5097 (tpt) cc_final: 0.4771 (mmt) REVERT: A 193 MET cc_start: 0.3467 (mmm) cc_final: 0.2992 (mmp) REVERT: B 148 MET cc_start: 0.8868 (pmm) cc_final: 0.8542 (pmm) REVERT: B 235 MET cc_start: 0.8741 (ppp) cc_final: 0.8316 (ppp) REVERT: B 289 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8308 (tp) REVERT: C 168 MET cc_start: 0.6147 (mpp) cc_final: 0.5931 (mpp) REVERT: C 173 THR cc_start: 0.5954 (OUTLIER) cc_final: 0.5598 (m) REVERT: C 217 MET cc_start: 0.2199 (OUTLIER) cc_final: 0.1908 (mmm) REVERT: D 128 ILE cc_start: 0.8285 (mt) cc_final: 0.8063 (mt) REVERT: D 259 MET cc_start: 0.8913 (mmm) cc_final: 0.8183 (mmt) REVERT: E 59 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6450 (t80) REVERT: E 160 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7963 (t70) REVERT: E 217 MET cc_start: 0.2689 (tpt) cc_final: 0.2016 (tpp) REVERT: E 220 LEU cc_start: 0.2512 (tp) cc_final: 0.2151 (mt) REVERT: F 27 MET cc_start: 0.8071 (tpp) cc_final: 0.7684 (ptt) REVERT: H 1 MET cc_start: 0.4788 (mpp) cc_final: 0.3882 (mmp) REVERT: I 175 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5539 (pt0) REVERT: I 486 MET cc_start: -0.1350 (mpp) cc_final: -0.2273 (mmt) REVERT: J 105 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.4974 (mm) REVERT: J 235 GLU cc_start: 0.6534 (mm-30) cc_final: 0.5821 (mm-30) REVERT: J 317 MET cc_start: 0.1265 (mmp) cc_final: -0.1188 (tpp) REVERT: J 538 ILE cc_start: 0.8604 (mm) cc_final: 0.8358 (mp) REVERT: J 578 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: J 579 ARG cc_start: 0.7720 (tmt170) cc_final: 0.7424 (ttp-110) REVERT: J 592 HIS cc_start: 0.8144 (m-70) cc_final: 0.7896 (m-70) REVERT: J 660 ILE cc_start: 0.9251 (mt) cc_final: 0.9000 (mp) REVERT: J 664 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7899 (tmtt) REVERT: J 722 GLN cc_start: 0.7995 (mt0) cc_final: 0.7770 (tm-30) REVERT: J 767 SER cc_start: 0.8489 (m) cc_final: 0.8026 (t) outliers start: 119 outliers final: 79 residues processed: 361 average time/residue: 0.1694 time to fit residues: 103.3826 Evaluate side-chains 331 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 154 HIS Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 681 ILE Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 236 optimal weight: 5.9990 chunk 163 optimal weight: 40.0000 chunk 214 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 385 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN D 478 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 ASN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 HIS ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** 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 = 0.4510 r_free = 0.4510 target = 0.106944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.090854 restraints weight = 240673.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.090228 restraints weight = 131165.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.090621 restraints weight = 113488.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.090567 restraints weight = 104093.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.090707 restraints weight = 94164.819| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32550 Z= 0.141 Angle : 0.708 13.385 44084 Z= 0.357 Chirality : 0.045 0.210 4856 Planarity : 0.005 0.077 5610 Dihedral : 5.395 54.206 4326 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.19 % Allowed : 22.83 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.81 (0.13), residues: 3894 helix: -0.43 (0.12), residues: 1824 sheet: -1.77 (0.25), residues: 397 loop : -1.86 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 139 TYR 0.025 0.002 TYR D 241 PHE 0.029 0.002 PHE J 197 TRP 0.017 0.001 TRP I 245 HIS 0.014 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00313 (32542) covalent geometry : angle 0.70804 (44068) SS BOND : bond 0.00444 ( 8) SS BOND : angle 0.90224 ( 16) hydrogen bonds : bond 0.04028 ( 1348) hydrogen bonds : angle 5.57150 ( 3807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 259 time to evaluate : 1.288 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 158 MET cc_start: -0.2145 (OUTLIER) cc_final: -0.2466 (pmm) REVERT: B 235 MET cc_start: 0.8737 (ppp) cc_final: 0.8308 (ppp) REVERT: B 289 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8251 (tp) REVERT: C 145 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: C 168 MET cc_start: 0.6298 (mpp) cc_final: 0.6068 (mpp) REVERT: C 173 THR cc_start: 0.6132 (OUTLIER) cc_final: 0.5768 (m) REVERT: C 217 MET cc_start: 0.1788 (OUTLIER) cc_final: 0.1233 (mmm) REVERT: D 1 MET cc_start: 0.4833 (mpp) cc_final: 0.3621 (mpp) REVERT: D 128 ILE cc_start: 0.8319 (mt) cc_final: 0.8111 (mt) REVERT: D 259 MET cc_start: 0.8902 (mmm) cc_final: 0.8554 (mmp) REVERT: E 59 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6718 (t80) REVERT: E 160 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8034 (t0) REVERT: E 217 MET cc_start: 0.2974 (tpt) cc_final: 0.2341 (tpp) REVERT: E 220 LEU cc_start: 0.2630 (tp) cc_final: 0.2167 (mt) REVERT: F 27 MET cc_start: 0.8113 (tpp) cc_final: 0.7715 (ptt) REVERT: H 1 MET cc_start: 0.4961 (mpp) cc_final: 0.4114 (mmp) REVERT: I 175 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5370 (pt0) REVERT: I 486 MET cc_start: -0.1389 (mpp) cc_final: -0.2277 (mmt) REVERT: J 84 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7185 (t0) REVERT: J 105 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5061 (mm) REVERT: J 175 GLU cc_start: 0.7148 (mp0) cc_final: 0.6548 (pp20) REVERT: J 193 LEU cc_start: 0.1308 (OUTLIER) cc_final: 0.0994 (pp) REVERT: J 235 GLU cc_start: 0.6474 (mm-30) cc_final: 0.5869 (mm-30) REVERT: J 317 MET cc_start: 0.1533 (mmp) cc_final: -0.1112 (tpp) REVERT: J 324 MET cc_start: -0.1046 (tmm) cc_final: -0.2043 (ttt) REVERT: J 533 ILE cc_start: 0.9285 (tt) cc_final: 0.9040 (mp) REVERT: J 538 ILE cc_start: 0.8685 (mm) cc_final: 0.8448 (mp) REVERT: J 568 ASP cc_start: 0.6418 (t70) cc_final: 0.6187 (t70) REVERT: J 578 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: J 579 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7339 (ttp-110) REVERT: J 592 HIS cc_start: 0.8199 (m-70) cc_final: 0.7918 (m-70) REVERT: J 628 MET cc_start: 0.6440 (mmt) cc_final: 0.6199 (mmt) REVERT: J 722 GLN cc_start: 0.8011 (mt0) cc_final: 0.7762 (tm-30) REVERT: J 767 SER cc_start: 0.8397 (m) cc_final: 0.7912 (t) outliers start: 111 outliers final: 78 residues processed: 354 average time/residue: 0.1711 time to fit residues: 102.9279 Evaluate side-chains 333 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 243 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 174 GLU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 681 ILE Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 322 optimal weight: 30.0000 chunk 272 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 94 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS B 24 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS F 412 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** 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 = 0.4465 r_free = 0.4465 target = 0.103991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.087478 restraints weight = 231749.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.086046 restraints weight = 168086.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.086601 restraints weight = 128584.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.086625 restraints weight = 105641.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.086655 restraints weight = 103294.047| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 32550 Z= 0.220 Angle : 0.777 16.096 44084 Z= 0.397 Chirality : 0.048 0.364 4856 Planarity : 0.005 0.052 5610 Dihedral : 5.611 50.627 4326 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.34 % Allowed : 23.15 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.97 (0.13), residues: 3894 helix: -0.51 (0.12), residues: 1813 sheet: -1.92 (0.25), residues: 380 loop : -1.98 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 290 TYR 0.044 0.002 TYR B 341 PHE 0.035 0.002 PHE H 383 TRP 0.021 0.002 TRP I 245 HIS 0.017 0.002 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00494 (32542) covalent geometry : angle 0.77660 (44068) SS BOND : bond 0.00740 ( 8) SS BOND : angle 1.26582 ( 16) hydrogen bonds : bond 0.04385 ( 1348) hydrogen bonds : angle 5.81896 ( 3807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 238 time to evaluate : 1.210 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: A 169 MET cc_start: 0.5430 (tpt) cc_final: 0.5089 (mmt) REVERT: A 193 MET cc_start: 0.3634 (mmm) cc_final: 0.2942 (mmp) REVERT: B 235 MET cc_start: 0.8653 (ppp) cc_final: 0.8240 (ppp) REVERT: B 259 MET cc_start: 0.7838 (tpp) cc_final: 0.7283 (tmm) REVERT: B 289 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8331 (tp) REVERT: C 145 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: C 168 MET cc_start: 0.6256 (mpp) cc_final: 0.6035 (mpp) REVERT: C 173 THR cc_start: 0.6045 (OUTLIER) cc_final: 0.5661 (m) REVERT: C 217 MET cc_start: 0.1717 (mmp) cc_final: 0.1396 (mmp) REVERT: D 1 MET cc_start: 0.4332 (mpp) cc_final: 0.3030 (mpp) REVERT: D 259 MET cc_start: 0.8898 (mmm) cc_final: 0.8558 (mmp) REVERT: E 59 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6793 (t80) REVERT: E 217 MET cc_start: 0.2836 (tpt) cc_final: 0.2237 (tpp) REVERT: E 220 LEU cc_start: 0.2908 (tp) cc_final: 0.2382 (mt) REVERT: F 27 MET cc_start: 0.8203 (tpp) cc_final: 0.7741 (ptt) REVERT: G 145 TYR cc_start: 0.7136 (m-80) cc_final: 0.6808 (m-80) REVERT: G 183 ARG cc_start: 0.9466 (mmm-85) cc_final: 0.9028 (tpm170) REVERT: H 1 MET cc_start: 0.4959 (mpp) cc_final: 0.3996 (mmp) REVERT: I 175 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5526 (pt0) REVERT: I 486 MET cc_start: -0.0814 (mpp) cc_final: -0.1690 (mmt) REVERT: I 650 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.5993 (pptt) REVERT: I 782 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: J 105 ILE cc_start: 0.5226 (OUTLIER) cc_final: 0.4802 (mm) REVERT: J 175 GLU cc_start: 0.7051 (mp0) cc_final: 0.6543 (pp20) REVERT: J 193 LEU cc_start: 0.1522 (OUTLIER) cc_final: 0.1219 (pp) REVERT: J 224 TYR cc_start: 0.7070 (m-80) cc_final: 0.6443 (m-80) REVERT: J 235 GLU cc_start: 0.6683 (mm-30) cc_final: 0.5983 (mm-30) REVERT: J 317 MET cc_start: 0.1329 (mmp) cc_final: -0.1140 (tpp) REVERT: J 549 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7191 (mt) REVERT: J 579 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7543 (ttp-110) REVERT: J 592 HIS cc_start: 0.8154 (m-70) cc_final: 0.7865 (m-70) REVERT: J 628 MET cc_start: 0.6904 (mmt) cc_final: 0.6668 (mmt) REVERT: J 722 GLN cc_start: 0.8032 (mt0) cc_final: 0.7782 (tm-30) REVERT: J 767 SER cc_start: 0.8396 (m) cc_final: 0.7952 (t) outliers start: 116 outliers final: 87 residues processed: 337 average time/residue: 0.1636 time to fit residues: 94.2205 Evaluate side-chains 329 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 232 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 154 HIS Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 782 PHE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 549 ILE Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 590 SER Chi-restraints excluded: chain J residue 681 ILE Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 744 THR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 6 optimal weight: 20.0000 chunk 267 optimal weight: 0.0060 chunk 260 optimal weight: 0.0670 chunk 150 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 chunk 334 optimal weight: 9.9990 overall best weight: 1.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS F 478 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.107108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.090438 restraints weight = 236675.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.090014 restraints weight = 138183.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.090172 restraints weight = 107989.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.090288 restraints weight = 96011.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.090587 restraints weight = 85179.435| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32550 Z= 0.138 Angle : 0.732 15.186 44084 Z= 0.368 Chirality : 0.046 0.318 4856 Planarity : 0.005 0.054 5610 Dihedral : 5.364 54.522 4326 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.53 % Allowed : 23.92 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.71 (0.13), residues: 3894 helix: -0.34 (0.12), residues: 1822 sheet: -1.69 (0.25), residues: 390 loop : -1.82 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.030 0.002 TYR B 360 PHE 0.030 0.002 PHE J 197 TRP 0.016 0.001 TRP I 245 HIS 0.014 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00308 (32542) covalent geometry : angle 0.73211 (44068) SS BOND : bond 0.00383 ( 8) SS BOND : angle 0.99223 ( 16) hydrogen bonds : bond 0.04021 ( 1348) hydrogen bonds : angle 5.55650 ( 3807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 265 time to evaluate : 1.164 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: A 169 MET cc_start: 0.5297 (tpt) cc_final: 0.4994 (mmt) REVERT: A 193 MET cc_start: 0.3708 (mmm) cc_final: 0.3097 (mmp) REVERT: B 235 MET cc_start: 0.8727 (ppp) cc_final: 0.8288 (ppp) REVERT: B 259 MET cc_start: 0.7780 (tpp) cc_final: 0.7210 (tmm) REVERT: B 289 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 145 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7098 (m-80) REVERT: C 173 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5633 (m) REVERT: D 1 MET cc_start: 0.4792 (mpp) cc_final: 0.3567 (mpp) REVERT: D 259 MET cc_start: 0.8944 (mmm) cc_final: 0.8629 (mmp) REVERT: E 59 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6757 (t80) REVERT: E 217 MET cc_start: 0.2811 (tpt) cc_final: 0.2245 (tpp) REVERT: E 220 LEU cc_start: 0.2661 (tp) cc_final: 0.2205 (mt) REVERT: F 27 MET cc_start: 0.8156 (tpp) cc_final: 0.7829 (ptt) REVERT: F 276 MET cc_start: 0.8757 (mmm) cc_final: 0.8453 (mmm) REVERT: G 145 TYR cc_start: 0.6833 (m-80) cc_final: 0.6515 (m-80) REVERT: G 183 ARG cc_start: 0.9434 (mmm-85) cc_final: 0.8823 (tpm170) REVERT: H 1 MET cc_start: 0.5378 (mpp) cc_final: 0.4576 (mmp) REVERT: I 175 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5318 (pt0) REVERT: I 679 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6317 (p) REVERT: J 105 ILE cc_start: 0.5693 (OUTLIER) cc_final: 0.5194 (mm) REVERT: J 175 GLU cc_start: 0.7324 (mp0) cc_final: 0.6917 (pp20) REVERT: J 193 LEU cc_start: 0.1381 (OUTLIER) cc_final: 0.1050 (pp) REVERT: J 235 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5649 (mm-30) REVERT: J 317 MET cc_start: 0.1770 (mmp) cc_final: -0.0636 (tpp) REVERT: J 324 MET cc_start: -0.0856 (tmm) cc_final: -0.1843 (ttt) REVERT: J 538 ILE cc_start: 0.8747 (mm) cc_final: 0.8527 (mp) REVERT: J 578 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: J 579 ARG cc_start: 0.7746 (tmt170) cc_final: 0.7382 (ttp-110) REVERT: J 592 HIS cc_start: 0.8180 (m-70) cc_final: 0.7878 (m-70) REVERT: J 628 MET cc_start: 0.6937 (mmt) cc_final: 0.6704 (mmt) REVERT: J 767 SER cc_start: 0.8261 (m) cc_final: 0.7837 (t) outliers start: 88 outliers final: 66 residues processed: 340 average time/residue: 0.1792 time to fit residues: 102.7178 Evaluate side-chains 323 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 248 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 587 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 34 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 chunk 87 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 36 optimal weight: 40.0000 chunk 66 optimal weight: 0.3980 chunk 346 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.090297 restraints weight = 240002.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.089626 restraints weight = 127342.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.089901 restraints weight = 98968.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.090033 restraints weight = 89107.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.090089 restraints weight = 79435.381| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32550 Z= 0.152 Angle : 0.726 13.554 44084 Z= 0.366 Chirality : 0.046 0.351 4856 Planarity : 0.005 0.051 5610 Dihedral : 5.328 51.650 4326 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.59 % Allowed : 24.09 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.70 (0.13), residues: 3894 helix: -0.32 (0.12), residues: 1825 sheet: -1.66 (0.25), residues: 385 loop : -1.84 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 139 TYR 0.029 0.002 TYR D 241 PHE 0.024 0.002 PHE G 122 TRP 0.023 0.001 TRP I 327 HIS 0.015 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00347 (32542) covalent geometry : angle 0.72580 (44068) SS BOND : bond 0.00530 ( 8) SS BOND : angle 1.05606 ( 16) hydrogen bonds : bond 0.04002 ( 1348) hydrogen bonds : angle 5.54922 ( 3807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6579.49 seconds wall clock time: 115 minutes 3.52 seconds (6903.52 seconds total)