Starting phenix.real_space_refine on Mon Aug 25 13:23:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5z_22067/08_2025/6x5z_22067.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 159 5.16 5 C 18019 2.51 5 N 4810 2.21 5 O 5419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 213 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "G" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "A" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "C" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "J" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.64, per 1000 atoms: 0.20 Number of scatterers: 28416 At special positions: 0 Unit cell: (159, 124.02, 248.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 159 16.00 P 6 15.00 Mg 3 11.99 O 5419 8.00 N 4810 7.00 C 18019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6676 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 45 sheets defined 53.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.916A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.769A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.572A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.807A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.849A pdb=" N LEU B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 4.100A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.046A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.705A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.532A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'O' and resid 46 through 210 removed outlier: 4.175A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 111 removed outlier: 3.846A pdb=" N VAL G 101 " --> pdb=" O HIS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.953A pdb=" N VAL G 139 " --> pdb=" O ASN G 135 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 135 through 140' Processing helix chain 'G' and resid 153 through 169 removed outlier: 3.802A pdb=" N ILE G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 187 through 198 removed outlier: 4.206A pdb=" N GLN G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE G 198 " --> pdb=" O TYR G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 230 removed outlier: 3.892A pdb=" N GLN G 222 " --> pdb=" O ASP G 218 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Proline residue: G 225 - end of helix removed outlier: 4.087A pdb=" N ALA G 229 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 274 removed outlier: 3.665A pdb=" N ARG G 272 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 274 " --> pdb=" O SER G 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 269 through 274' Processing helix chain 'G' and resid 283 through 291 removed outlier: 3.968A pdb=" N TYR G 287 " --> pdb=" O TYR G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 302 removed outlier: 3.963A pdb=" N LEU G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 310 through 315 removed outlier: 3.805A pdb=" N GLN G 315 " --> pdb=" O ALA G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 339 removed outlier: 4.600A pdb=" N GLU G 328 " --> pdb=" O ASP G 324 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N MET G 330 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 359 removed outlier: 3.795A pdb=" N TYR G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'G' and resid 377 through 388 removed outlier: 3.525A pdb=" N ALA G 381 " --> pdb=" O GLY G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 401 removed outlier: 3.504A pdb=" N LEU G 395 " --> pdb=" O ASN G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 447 removed outlier: 3.743A pdb=" N GLY G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 504 removed outlier: 3.523A pdb=" N LEU G 476 " --> pdb=" O SER G 472 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 485 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN G 486 " --> pdb=" O ASN G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 526 removed outlier: 4.695A pdb=" N CYS G 520 " --> pdb=" O ASP G 516 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU G 523 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 540 removed outlier: 3.594A pdb=" N MET G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 557 removed outlier: 3.612A pdb=" N LYS G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU G 557 " --> pdb=" O PHE G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 598 Processing helix chain 'G' and resid 602 through 609 removed outlier: 3.967A pdb=" N VAL G 606 " --> pdb=" O ASN G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 613 through 622 removed outlier: 3.646A pdb=" N LEU G 617 " --> pdb=" O SER G 613 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA G 622 " --> pdb=" O SER G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 664 removed outlier: 3.562A pdb=" N LEU G 650 " --> pdb=" O THR G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 685 through 697 removed outlier: 3.702A pdb=" N VAL G 689 " --> pdb=" O ASP G 685 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS G 691 " --> pdb=" O PRO G 687 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 697 " --> pdb=" O LEU G 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 697 through 708 Processing helix chain 'G' and resid 715 through 722 Processing helix chain 'G' and resid 737 through 741 removed outlier: 3.722A pdb=" N GLY G 741 " --> pdb=" O SER G 738 " (cutoff:3.500A) Processing helix chain 'G' and resid 771 through 776 removed outlier: 3.552A pdb=" N GLU G 775 " --> pdb=" O GLY G 771 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET G 776 " --> pdb=" O LEU G 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 771 through 776' Processing helix chain 'P' and resid 46 through 210 removed outlier: 3.651A pdb=" N VAL P 170 " --> pdb=" O ALA P 166 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.917A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.769A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.572A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.807A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.849A pdb=" N LEU A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 4.101A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.046A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.705A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.531A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'D' and resid 97 through 111 removed outlier: 3.845A pdb=" N VAL D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.953A pdb=" N VAL D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA D 140 " --> pdb=" O ALA D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 140' Processing helix chain 'D' and resid 153 through 169 removed outlier: 3.803A pdb=" N ILE D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 187 through 198 removed outlier: 4.206A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE D 198 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.892A pdb=" N GLN D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Proline residue: D 225 - end of helix removed outlier: 4.087A pdb=" N ALA D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 removed outlier: 3.665A pdb=" N ARG D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL D 273 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 274 " --> pdb=" O SER D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 274' Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.969A pdb=" N TYR D 287 " --> pdb=" O TYR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 removed outlier: 3.962A pdb=" N LEU D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.806A pdb=" N GLN D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 339 removed outlier: 4.600A pdb=" N GLU D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N MET D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 359 removed outlier: 3.795A pdb=" N TYR D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.524A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.503A pdb=" N LEU D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 447 removed outlier: 3.744A pdb=" N GLY D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 504 removed outlier: 3.523A pdb=" N LEU D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 526 removed outlier: 4.696A pdb=" N CYS D 520 " --> pdb=" O ASP D 516 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 540 removed outlier: 3.594A pdb=" N MET D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.612A pdb=" N LYS D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 598 Processing helix chain 'D' and resid 602 through 609 removed outlier: 3.967A pdb=" N VAL D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 622 removed outlier: 3.646A pdb=" N LEU D 617 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 664 removed outlier: 3.561A pdb=" N LEU D 650 " --> pdb=" O THR D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.703A pdb=" N VAL D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS D 691 " --> pdb=" O PRO D 687 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 708 Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 737 through 741 removed outlier: 3.722A pdb=" N GLY D 741 " --> pdb=" O SER D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 776 removed outlier: 3.552A pdb=" N GLU D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 776 " --> pdb=" O LEU D 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 771 through 776' Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.916A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.769A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.571A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.808A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.849A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 4.100A pdb=" N ARG C 210 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.046A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.705A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.532A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'J' and resid 97 through 111 removed outlier: 3.846A pdb=" N VAL J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 140 removed outlier: 3.954A pdb=" N VAL J 139 " --> pdb=" O ASN J 135 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 140' Processing helix chain 'J' and resid 153 through 169 removed outlier: 3.802A pdb=" N ILE J 157 " --> pdb=" O HIS J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 183 Processing helix chain 'J' and resid 187 through 198 removed outlier: 4.206A pdb=" N GLN J 193 " --> pdb=" O LYS J 189 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE J 198 " --> pdb=" O TYR J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 230 removed outlier: 3.892A pdb=" N GLN J 222 " --> pdb=" O ASP J 218 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA J 223 " --> pdb=" O GLN J 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN J 224 " --> pdb=" O ILE J 220 " (cutoff:3.500A) Proline residue: J 225 - end of helix removed outlier: 4.086A pdb=" N ALA J 229 " --> pdb=" O PRO J 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 274 removed outlier: 3.665A pdb=" N ARG J 272 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL J 273 " --> pdb=" O LYS J 270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE J 274 " --> pdb=" O SER J 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 269 through 274' Processing helix chain 'J' and resid 283 through 291 removed outlier: 3.968A pdb=" N TYR J 287 " --> pdb=" O TYR J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 302 removed outlier: 3.964A pdb=" N LEU J 298 " --> pdb=" O LYS J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 315 removed outlier: 3.805A pdb=" N GLN J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 339 removed outlier: 4.601A pdb=" N GLU J 328 " --> pdb=" O ASP J 324 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N MET J 330 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 359 removed outlier: 3.795A pdb=" N TYR J 350 " --> pdb=" O LYS J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.524A pdb=" N ALA J 381 " --> pdb=" O GLY J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 401 removed outlier: 3.504A pdb=" N LEU J 395 " --> pdb=" O ASN J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 447 removed outlier: 3.743A pdb=" N GLY J 425 " --> pdb=" O VAL J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 504 removed outlier: 3.523A pdb=" N LEU J 476 " --> pdb=" O SER J 472 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 485 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN J 486 " --> pdb=" O ASN J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 526 removed outlier: 4.695A pdb=" N CYS J 520 " --> pdb=" O ASP J 516 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU J 523 " --> pdb=" O ALA J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 540 removed outlier: 3.594A pdb=" N MET J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 557 removed outlier: 3.612A pdb=" N LYS J 549 " --> pdb=" O ASP J 545 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU J 557 " --> pdb=" O PHE J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 592 through 598 Processing helix chain 'J' and resid 602 through 609 removed outlier: 3.967A pdb=" N VAL J 606 " --> pdb=" O ASN J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 622 removed outlier: 3.646A pdb=" N LEU J 617 " --> pdb=" O SER J 613 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA J 622 " --> pdb=" O SER J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 664 removed outlier: 3.562A pdb=" N LEU J 650 " --> pdb=" O THR J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 685 through 697 removed outlier: 3.702A pdb=" N VAL J 689 " --> pdb=" O ASP J 685 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS J 691 " --> pdb=" O PRO J 687 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY J 697 " --> pdb=" O LEU J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 708 Processing helix chain 'J' and resid 715 through 722 Processing helix chain 'J' and resid 737 through 741 removed outlier: 3.722A pdb=" N GLY J 741 " --> pdb=" O SER J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 771 through 776 removed outlier: 3.552A pdb=" N GLU J 775 " --> pdb=" O GLY J 771 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET J 776 " --> pdb=" O LEU J 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 771 through 776' Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.678A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.733A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 105 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 135 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 107 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.903A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.613A pdb=" N VAL G 47 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 51 through 55 removed outlier: 5.310A pdb=" N ILE G 51 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU G 62 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER G 53 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU G 55 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 116 through 118 Processing sheet with id=AB1, first strand: chain 'G' and resid 258 through 260 removed outlier: 3.887A pdb=" N SER G 260 " --> pdb=" O HIS G 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 258 through 260 removed outlier: 3.887A pdb=" N SER G 260 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP G 461 " --> pdb=" O LYS G 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE G 250 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER G 173 " --> pdb=" O HIS G 668 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL G 670 " --> pdb=" O SER G 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU G 175 " --> pdb=" O VAL G 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AB4, first strand: chain 'G' and resid 363 through 366 removed outlier: 3.853A pdb=" N LYS G 363 " --> pdb=" O ASP G 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 563 through 564 Processing sheet with id=AB6, first strand: chain 'G' and resid 713 through 714 Processing sheet with id=AB7, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.678A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.733A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 105 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 135 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 107 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.903A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.613A pdb=" N VAL D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 51 through 55 removed outlier: 5.310A pdb=" N ILE D 51 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU D 62 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 53 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 55 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AC7, first strand: chain 'D' and resid 258 through 260 removed outlier: 3.887A pdb=" N SER D 260 " --> pdb=" O HIS D 251 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 258 through 260 removed outlier: 3.887A pdb=" N SER D 260 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 461 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 250 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER D 173 " --> pdb=" O HIS D 668 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 670 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU D 175 " --> pdb=" O VAL D 670 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 232 through 233 Processing sheet with id=AD1, first strand: chain 'D' and resid 363 through 366 removed outlier: 3.853A pdb=" N LYS D 363 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 563 through 564 Processing sheet with id=AD3, first strand: chain 'D' and resid 713 through 714 Processing sheet with id=AD4, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.677A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.734A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 105 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 135 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.903A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 47 through 49 removed outlier: 3.613A pdb=" N VAL J 47 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 55 removed outlier: 5.310A pdb=" N ILE J 51 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU J 62 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER J 53 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU J 55 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 116 through 118 Processing sheet with id=AE4, first strand: chain 'J' and resid 258 through 260 removed outlier: 3.888A pdb=" N SER J 260 " --> pdb=" O HIS J 251 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 258 through 260 removed outlier: 3.888A pdb=" N SER J 260 " --> pdb=" O HIS J 251 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP J 461 " --> pdb=" O LYS J 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE J 250 " --> pdb=" O ILE J 457 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER J 173 " --> pdb=" O HIS J 668 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL J 670 " --> pdb=" O SER J 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU J 175 " --> pdb=" O VAL J 670 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 232 through 233 Processing sheet with id=AE7, first strand: chain 'J' and resid 363 through 366 removed outlier: 3.854A pdb=" N LYS J 363 " --> pdb=" O ASP J 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 563 through 564 Processing sheet with id=AE9, first strand: chain 'J' and resid 713 through 714 1368 hydrogen bonds defined for protein. 3852 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: 5.46 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8990 1.34 - 1.46: 6746 1.46 - 1.58: 12956 1.58 - 1.71: 9 1.71 - 1.83: 277 Bond restraints: 28978 Sorted by residual: bond pdb=" ND1 HIS O 153 " pdb=" CE1 HIS O 153 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" ND1 HIS P 153 " pdb=" CE1 HIS P 153 " ideal model delta sigma weight residual 1.321 1.353 -0.032 1.00e-02 1.00e+04 1.03e+01 bond pdb=" CD ARG P 160 " pdb=" NE ARG P 160 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CD ARG P 90 " pdb=" NE ARG P 90 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 9.07e+00 bond pdb=" CD ARG O 160 " pdb=" NE ARG O 160 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 8.96e+00 ... (remaining 28973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 36122 1.87 - 3.75: 2533 3.75 - 5.62: 366 5.62 - 7.49: 67 7.49 - 9.37: 20 Bond angle restraints: 39108 Sorted by residual: angle pdb=" C GLY D 708 " pdb=" N PHE D 709 " pdb=" CA PHE D 709 " ideal model delta sigma weight residual 120.09 128.07 -7.98 1.25e+00 6.40e-01 4.08e+01 angle pdb=" C GLY G 708 " pdb=" N PHE G 709 " pdb=" CA PHE G 709 " ideal model delta sigma weight residual 120.09 128.05 -7.96 1.25e+00 6.40e-01 4.06e+01 angle pdb=" C GLY J 708 " pdb=" N PHE J 709 " pdb=" CA PHE J 709 " ideal model delta sigma weight residual 120.09 128.04 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" N ILE A 287 " pdb=" CA ILE A 287 " pdb=" C ILE A 287 " ideal model delta sigma weight residual 112.29 106.89 5.40 9.40e-01 1.13e+00 3.30e+01 angle pdb=" N ILE C 287 " pdb=" CA ILE C 287 " pdb=" C ILE C 287 " ideal model delta sigma weight residual 112.29 106.89 5.40 9.40e-01 1.13e+00 3.30e+01 ... (remaining 39103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15917 17.98 - 35.96: 1359 35.96 - 53.94: 208 53.94 - 71.92: 93 71.92 - 89.89: 34 Dihedral angle restraints: 17611 sinusoidal: 7259 harmonic: 10352 Sorted by residual: dihedral pdb=" CA ASN C 111 " pdb=" C ASN C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ASN B 111 " pdb=" C ASN B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ASN A 111 " pdb=" C ASN A 111 " pdb=" N PRO A 112 " pdb=" CA PRO A 112 " ideal model delta harmonic sigma weight residual 180.00 147.17 32.83 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 17608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3238 0.055 - 0.110: 856 0.110 - 0.165: 152 0.165 - 0.220: 33 0.220 - 0.276: 11 Chirality restraints: 4290 Sorted by residual: chirality pdb=" CA THR O 108 " pdb=" N THR O 108 " pdb=" C THR O 108 " pdb=" CB THR O 108 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG O 182 " pdb=" N ARG O 182 " pdb=" C ARG O 182 " pdb=" CB ARG O 182 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR P 201 " pdb=" N THR P 201 " pdb=" C THR P 201 " pdb=" CB THR P 201 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4287 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 162 " 0.104 2.00e-02 2.50e+03 5.34e-02 5.71e+01 pdb=" CG TYR P 162 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR P 162 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR P 162 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR P 162 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR P 162 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR P 162 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR P 162 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 356 " -0.034 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP C 356 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP C 356 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 356 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 356 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 356 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 356 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 356 " -0.034 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP B 356 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 356 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 356 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 356 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 356 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 356 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 356 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 356 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 356 " -0.004 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 9 1.95 - 2.69: 981 2.69 - 3.43: 43917 3.43 - 4.16: 64261 4.16 - 4.90: 113613 Nonbonded interactions: 222781 Sorted by model distance: nonbonded pdb=" OD2 ASP B 244 " pdb=" CG2 ILE A 287 " model vdw 1.215 3.460 nonbonded pdb=" OE1 GLN O 93 " pdb=" OE1 GLN D 368 " model vdw 1.315 3.040 nonbonded pdb=" O VAL B 45 " pdb=" OH TYR A 143 " model vdw 1.378 3.040 nonbonded pdb=" CD GLN O 93 " pdb=" OE1 GLN D 368 " model vdw 1.452 2.616 nonbonded pdb=" NH1 ARG B 290 " pdb=" OD2 ASP C 244 " model vdw 1.552 3.120 ... (remaining 222776 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.680 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.008 0.377 28985 Z= 0.522 Angle : 1.072 9.366 39108 Z= 0.651 Chirality : 0.053 0.276 4290 Planarity : 0.007 0.129 5058 Dihedral : 14.747 89.894 10935 Min Nonbonded Distance : 1.215 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.29 % Favored : 89.45 % Rotamer: Outliers : 0.10 % Allowed : 1.04 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.13), residues: 3526 helix: 0.02 (0.12), residues: 1552 sheet: -1.22 (0.30), residues: 306 loop : -2.24 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 434 TYR 0.104 0.003 TYR P 162 PHE 0.024 0.003 PHE J 540 TRP 0.080 0.004 TRP C 356 HIS 0.014 0.002 HIS D 651 Details of bonding type rmsd covalent geometry : bond 0.00768 (28978) covalent geometry : angle 1.07213 (39108) hydrogen bonds : bond 0.18954 ( 1365) hydrogen bonds : angle 7.37910 ( 3852) Misc. bond : bond 0.22518 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1026 time to evaluate : 1.117 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: 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 76 ILE cc_start: 0.8812 (mt) cc_final: 0.8529 (mt) REVERT: B 87 HIS cc_start: 0.8865 (t70) cc_final: 0.8594 (t-90) REVERT: B 94 LEU cc_start: 0.8202 (tt) cc_final: 0.7962 (mp) REVERT: B 148 THR cc_start: 0.8919 (t) cc_final: 0.8547 (m) REVERT: B 334 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5912 (mt-10) REVERT: B 364 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6802 (mm-30) REVERT: G 90 MET cc_start: 0.6630 (mmt) cc_final: 0.5755 (mmm) REVERT: G 218 ASP cc_start: 0.8042 (m-30) cc_final: 0.7718 (m-30) REVERT: G 295 PRO cc_start: 0.8400 (Cg_endo) cc_final: 0.8083 (Cg_exo) REVERT: G 427 LEU cc_start: 0.8868 (tt) cc_final: 0.8596 (tp) REVERT: G 435 MET cc_start: 0.8868 (ttt) cc_final: 0.8587 (ttm) REVERT: G 478 ILE cc_start: 0.8165 (mm) cc_final: 0.7895 (mm) REVERT: G 523 LEU cc_start: 0.8856 (tp) cc_final: 0.8488 (tp) REVERT: G 616 MET cc_start: 0.7202 (mtm) cc_final: 0.6977 (mtt) REVERT: G 687 PRO cc_start: 0.7875 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: G 704 ILE cc_start: 0.8806 (mm) cc_final: 0.8589 (mm) REVERT: G 745 LEU cc_start: 0.2387 (mt) cc_final: 0.2052 (pt) REVERT: A 244 ASP cc_start: 0.8375 (m-30) cc_final: 0.7546 (t0) REVERT: D 189 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7538 (mptt) REVERT: D 379 GLU cc_start: 0.7528 (pm20) cc_final: 0.7083 (pp20) REVERT: D 435 MET cc_start: 0.7581 (ttt) cc_final: 0.7255 (ttp) REVERT: D 502 LYS cc_start: 0.7454 (tmtt) cc_final: 0.7151 (mmmt) REVERT: D 547 THR cc_start: 0.8392 (p) cc_final: 0.8181 (t) REVERT: D 569 ILE cc_start: 0.6126 (pt) cc_final: 0.5868 (mm) REVERT: D 669 PHE cc_start: 0.5570 (m-80) cc_final: 0.4788 (m-80) REVERT: D 709 PHE cc_start: 0.1863 (m-80) cc_final: 0.1208 (m-10) REVERT: C 87 HIS cc_start: 0.7945 (t70) cc_final: 0.7627 (t-90) REVERT: C 178 LEU cc_start: 0.8714 (tp) cc_final: 0.8339 (pp) REVERT: C 296 ASN cc_start: 0.7866 (m-40) cc_final: 0.7501 (m-40) REVERT: C 323 SER cc_start: 0.8332 (p) cc_final: 0.7748 (t) REVERT: J 76 VAL cc_start: 0.7478 (t) cc_final: 0.7120 (p) REVERT: J 90 MET cc_start: 0.5474 (mmt) cc_final: 0.5022 (mmm) REVERT: J 218 ASP cc_start: 0.7300 (m-30) cc_final: 0.6611 (p0) REVERT: J 295 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: J 347 ASN cc_start: 0.6961 (p0) cc_final: 0.6712 (p0) REVERT: J 353 THR cc_start: 0.7907 (m) cc_final: 0.7490 (p) REVERT: J 357 MET cc_start: 0.7540 (mtt) cc_final: 0.7323 (mtt) REVERT: J 563 PHE cc_start: 0.7072 (t80) cc_final: 0.6823 (t80) REVERT: J 657 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8543 (mtpt) outliers start: 3 outliers final: 0 residues processed: 1027 average time/residue: 0.1803 time to fit residues: 284.7850 Evaluate side-chains 570 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0970 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 144 GLN G 153 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 GLN G 361 ASN G 372 GLN G 492 HIS ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 153 HIS ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 65 HIS D 126 ASN D 187 ASN D 251 HIS D 284 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 314 GLN C 371 HIS J 78 GLN J 126 ASN ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN J 251 HIS ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN J 372 GLN ** J 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.146498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115681 restraints weight = 75670.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115387 restraints weight = 50388.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116037 restraints weight = 37555.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116258 restraints weight = 30547.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116245 restraints weight = 29520.364| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28985 Z= 0.179 Angle : 0.792 10.022 39108 Z= 0.411 Chirality : 0.048 0.256 4290 Planarity : 0.006 0.083 5058 Dihedral : 6.888 68.907 3867 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.32 % Favored : 92.43 % Rotamer: Outliers : 0.39 % Allowed : 5.81 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 aren not related in a simple way. whole: -1.11 (0.14), residues: 3526 helix: 0.57 (0.12), residues: 1585 sheet: -1.04 (0.27), residues: 369 loop : -2.07 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 101 TYR 0.031 0.002 TYR P 60 PHE 0.029 0.002 PHE G 669 TRP 0.041 0.003 TRP A 356 HIS 0.013 0.002 HIS J 97 Details of bonding type rmsd covalent geometry : bond 0.00389 (28978) covalent geometry : angle 0.79214 (39108) hydrogen bonds : bond 0.05640 ( 1365) hydrogen bonds : angle 5.65451 ( 3852) Misc. bond : bond 0.01194 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 761 time to evaluate : 0.832 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: B 148 THR cc_start: 0.8905 (t) cc_final: 0.8672 (m) REVERT: B 169 TYR cc_start: 0.8111 (m-80) cc_final: 0.7682 (m-10) REVERT: B 184 ASP cc_start: 0.8207 (m-30) cc_final: 0.7784 (m-30) REVERT: B 283 MET cc_start: 0.8924 (mmm) cc_final: 0.8418 (mmt) REVERT: B 290 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8425 (mtt90) REVERT: B 334 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6145 (mt-10) REVERT: B 364 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7133 (mm-30) REVERT: O 198 LYS cc_start: 0.7940 (tttt) cc_final: 0.7684 (mmtt) REVERT: G 42 ASP cc_start: 0.7623 (t0) cc_final: 0.7422 (t0) REVERT: G 90 MET cc_start: 0.6231 (mmt) cc_final: 0.5816 (mmm) REVERT: G 98 GLU cc_start: 0.5947 (tt0) cc_final: 0.5398 (tt0) REVERT: G 116 THR cc_start: 0.8207 (m) cc_final: 0.7686 (t) REVERT: G 126 ASN cc_start: 0.8118 (m-40) cc_final: 0.7684 (m-40) REVERT: G 218 ASP cc_start: 0.8178 (m-30) cc_final: 0.7976 (m-30) REVERT: G 295 PRO cc_start: 0.8401 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: G 371 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8061 (pm20) REVERT: G 473 PHE cc_start: 0.8684 (t80) cc_final: 0.8449 (t80) REVERT: G 488 PHE cc_start: 0.7935 (t80) cc_final: 0.7687 (t80) REVERT: P 136 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8592 (mtpt) REVERT: A 120 THR cc_start: 0.8865 (t) cc_final: 0.8359 (t) REVERT: A 205 GLU cc_start: 0.7101 (pt0) cc_final: 0.6598 (mt-10) REVERT: A 211 ASP cc_start: 0.6648 (m-30) cc_final: 0.6338 (m-30) REVERT: A 244 ASP cc_start: 0.8204 (m-30) cc_final: 0.6980 (t0) REVERT: A 270 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6548 (mt-10) REVERT: A 334 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6264 (mm-30) REVERT: D 189 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7512 (mmtm) REVERT: D 244 PHE cc_start: 0.7476 (p90) cc_final: 0.6726 (p90) REVERT: D 362 MET cc_start: 0.8889 (mmp) cc_final: 0.8570 (mmm) REVERT: D 379 GLU cc_start: 0.7668 (pm20) cc_final: 0.7196 (pp20) REVERT: D 403 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7328 (mtp180) REVERT: D 534 LEU cc_start: 0.8317 (tp) cc_final: 0.7922 (tp) REVERT: D 547 THR cc_start: 0.8470 (p) cc_final: 0.8093 (t) REVERT: D 703 ARG cc_start: 0.7661 (tpt90) cc_final: 0.7087 (tpt90) REVERT: D 776 MET cc_start: 0.6027 (mpp) cc_final: 0.5799 (mpp) REVERT: C 47 MET cc_start: 0.7933 (ptp) cc_final: 0.7667 (ptp) REVERT: C 87 HIS cc_start: 0.8179 (t70) cc_final: 0.7937 (t-90) REVERT: C 147 ARG cc_start: 0.6576 (mtp85) cc_final: 0.6046 (mtp85) REVERT: C 296 ASN cc_start: 0.8368 (m-40) cc_final: 0.7818 (m-40) REVERT: C 323 SER cc_start: 0.8509 (p) cc_final: 0.8234 (t) REVERT: J 218 ASP cc_start: 0.7875 (m-30) cc_final: 0.6956 (p0) REVERT: J 239 ASP cc_start: 0.6728 (p0) cc_final: 0.6312 (p0) REVERT: J 337 ASP cc_start: 0.6520 (m-30) cc_final: 0.6310 (m-30) REVERT: J 390 LEU cc_start: 0.8157 (tt) cc_final: 0.7655 (tt) REVERT: J 424 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7991 (ptmm) REVERT: J 433 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8285 (tm-30) REVERT: J 563 PHE cc_start: 0.7641 (t80) cc_final: 0.7303 (t80) REVERT: J 612 SER cc_start: 0.5667 (m) cc_final: 0.4712 (p) outliers start: 12 outliers final: 2 residues processed: 770 average time/residue: 0.1686 time to fit residues: 207.0350 Evaluate side-chains 525 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 523 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 341 optimal weight: 0.4980 chunk 166 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN G 490 ASN G 661 ASN G 726 ASN P 153 HIS ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 78 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 HIS ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS J 126 ASN ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 661 ASN J 691 HIS ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.117548 restraints weight = 75670.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116617 restraints weight = 77813.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117703 restraints weight = 66123.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117655 restraints weight = 46907.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117886 restraints weight = 44170.276| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28985 Z= 0.182 Angle : 0.755 10.693 39108 Z= 0.391 Chirality : 0.047 0.251 4290 Planarity : 0.006 0.122 5058 Dihedral : 6.603 65.346 3867 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.06 % Rotamer: Outliers : 0.20 % Allowed : 4.50 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3526 helix: 0.83 (0.13), residues: 1555 sheet: -0.77 (0.28), residues: 360 loop : -2.05 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 125 TYR 0.045 0.002 TYR J 722 PHE 0.044 0.002 PHE G 669 TRP 0.047 0.003 TRP C 340 HIS 0.009 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00384 (28978) covalent geometry : angle 0.75468 (39108) hydrogen bonds : bond 0.05164 ( 1365) hydrogen bonds : angle 5.37450 ( 3852) Misc. bond : bond 0.00744 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 704 time to evaluate : 0.993 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: B 148 THR cc_start: 0.9015 (t) cc_final: 0.8683 (m) REVERT: B 184 ASP cc_start: 0.8107 (m-30) cc_final: 0.7704 (m-30) REVERT: B 279 TYR cc_start: 0.8453 (t80) cc_final: 0.8170 (t80) REVERT: B 283 MET cc_start: 0.8950 (mmm) cc_final: 0.8614 (mmt) REVERT: B 290 ARG cc_start: 0.8804 (mtt180) cc_final: 0.8331 (mtt90) REVERT: B 364 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6992 (mm-30) REVERT: O 68 GLN cc_start: 0.7545 (tm-30) cc_final: 0.6822 (mt0) REVERT: O 141 MET cc_start: 0.5669 (tpt) cc_final: 0.4631 (tpp) REVERT: G 90 MET cc_start: 0.6024 (mmt) cc_final: 0.5667 (mmm) REVERT: G 116 THR cc_start: 0.8098 (m) cc_final: 0.7663 (t) REVERT: G 126 ASN cc_start: 0.8009 (m-40) cc_final: 0.7639 (m-40) REVERT: G 174 ILE cc_start: 0.8793 (mp) cc_final: 0.8493 (mt) REVERT: G 244 PHE cc_start: 0.8717 (p90) cc_final: 0.8110 (p90) REVERT: G 295 PRO cc_start: 0.8388 (Cg_endo) cc_final: 0.7998 (Cg_exo) REVERT: P 139 GLU cc_start: 0.7304 (pt0) cc_final: 0.6752 (tp30) REVERT: A 81 ASP cc_start: 0.7851 (m-30) cc_final: 0.7516 (m-30) REVERT: A 179 ASP cc_start: 0.8177 (t0) cc_final: 0.7780 (t0) REVERT: A 205 GLU cc_start: 0.7042 (pt0) cc_final: 0.6536 (mt-10) REVERT: A 211 ASP cc_start: 0.6246 (m-30) cc_final: 0.6007 (m-30) REVERT: A 244 ASP cc_start: 0.8136 (m-30) cc_final: 0.6644 (t0) REVERT: A 270 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 325 MET cc_start: 0.8536 (mmp) cc_final: 0.8168 (mmp) REVERT: A 352 PHE cc_start: 0.8604 (t80) cc_final: 0.8164 (t80) REVERT: D 189 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7351 (mmtm) REVERT: D 244 PHE cc_start: 0.7454 (p90) cc_final: 0.6702 (p90) REVERT: D 362 MET cc_start: 0.8909 (mmp) cc_final: 0.8543 (mmp) REVERT: D 379 GLU cc_start: 0.7654 (pm20) cc_final: 0.7110 (pp20) REVERT: D 435 MET cc_start: 0.7272 (ttp) cc_final: 0.6890 (ttp) REVERT: D 534 LEU cc_start: 0.8436 (tp) cc_final: 0.8002 (tp) REVERT: D 539 MET cc_start: 0.6510 (mtp) cc_final: 0.6170 (mtp) REVERT: D 556 HIS cc_start: 0.4232 (m-70) cc_final: 0.3618 (m-70) REVERT: C 147 ARG cc_start: 0.6345 (mtp85) cc_final: 0.5884 (mtp85) REVERT: C 205 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7343 (mp0) REVERT: C 240 TYR cc_start: 0.8427 (t80) cc_final: 0.8222 (t80) REVERT: C 293 LEU cc_start: 0.8811 (mt) cc_final: 0.8570 (mt) REVERT: C 313 MET cc_start: 0.8946 (mmm) cc_final: 0.8493 (mmm) REVERT: J 84 PHE cc_start: 0.3976 (m-10) cc_final: 0.2923 (m-80) REVERT: J 165 MET cc_start: 0.7035 (mmm) cc_final: 0.6731 (tpt) REVERT: J 218 ASP cc_start: 0.7537 (m-30) cc_final: 0.6729 (p0) REVERT: J 357 MET cc_start: 0.8309 (mtt) cc_final: 0.6967 (mtt) REVERT: J 424 LYS cc_start: 0.8267 (ptmm) cc_final: 0.8026 (ptmm) REVERT: J 433 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8060 (tm-30) REVERT: J 563 PHE cc_start: 0.7290 (t80) cc_final: 0.6957 (t80) outliers start: 6 outliers final: 0 residues processed: 706 average time/residue: 0.1621 time to fit residues: 181.3942 Evaluate side-chains 502 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 58 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 153 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 ASN ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 661 ASN G 668 HIS ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 92 ASN A 225 ASN A 275 HIS A 314 GLN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 HIS ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 371 HIS J 126 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 ASN J 491 HIS ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.140810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.112787 restraints weight = 76105.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111234 restraints weight = 89580.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112517 restraints weight = 79764.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112438 restraints weight = 57158.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112729 restraints weight = 51921.426| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28985 Z= 0.240 Angle : 0.828 19.476 39108 Z= 0.430 Chirality : 0.050 0.260 4290 Planarity : 0.006 0.117 5058 Dihedral : 6.651 62.717 3867 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.80 % Favored : 92.12 % Rotamer: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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 aren not related in a simple way. whole: -1.01 (0.14), residues: 3526 helix: 0.67 (0.13), residues: 1544 sheet: -0.94 (0.27), residues: 366 loop : -1.99 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 369 TYR 0.050 0.002 TYR D 722 PHE 0.039 0.003 PHE G 669 TRP 0.059 0.003 TRP C 340 HIS 0.011 0.002 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00545 (28978) covalent geometry : angle 0.82778 (39108) hydrogen bonds : bond 0.05289 ( 1365) hydrogen bonds : angle 5.37817 ( 3852) Misc. bond : bond 0.00400 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 641 time to evaluate : 1.264 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: B 47 MET cc_start: 0.7916 (ptp) cc_final: 0.6827 (tpt) REVERT: B 148 THR cc_start: 0.9142 (t) cc_final: 0.8865 (m) REVERT: B 184 ASP cc_start: 0.8079 (m-30) cc_final: 0.7753 (m-30) REVERT: B 227 MET cc_start: 0.8140 (tpt) cc_final: 0.7879 (tpp) REVERT: B 283 MET cc_start: 0.9151 (mmm) cc_final: 0.8627 (mmt) REVERT: B 362 TYR cc_start: 0.8331 (t80) cc_final: 0.8018 (t80) REVERT: B 364 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7217 (mm-30) REVERT: O 127 MET cc_start: 0.6157 (tpt) cc_final: 0.5578 (mmm) REVERT: G 90 MET cc_start: 0.6116 (mmt) cc_final: 0.5779 (mmt) REVERT: G 126 ASN cc_start: 0.8245 (m-40) cc_final: 0.7902 (m-40) REVERT: G 174 ILE cc_start: 0.8926 (mp) cc_final: 0.8450 (mt) REVERT: G 295 PRO cc_start: 0.8460 (Cg_endo) cc_final: 0.8136 (Cg_exo) REVERT: G 497 GLU cc_start: 0.7751 (tp30) cc_final: 0.7550 (tp30) REVERT: G 704 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8206 (mp) REVERT: P 127 MET cc_start: 0.5456 (ptt) cc_final: 0.4352 (ptt) REVERT: P 139 GLU cc_start: 0.7484 (pt0) cc_final: 0.6824 (tp30) REVERT: A 120 THR cc_start: 0.8805 (t) cc_final: 0.8468 (t) REVERT: A 179 ASP cc_start: 0.8175 (t0) cc_final: 0.7607 (t0) REVERT: A 205 GLU cc_start: 0.7230 (pt0) cc_final: 0.7023 (mt-10) REVERT: A 211 ASP cc_start: 0.6551 (m-30) cc_final: 0.6350 (m-30) REVERT: A 244 ASP cc_start: 0.7635 (m-30) cc_final: 0.6551 (t0) REVERT: A 352 PHE cc_start: 0.8698 (t80) cc_final: 0.8303 (t80) REVERT: D 189 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7425 (mmtm) REVERT: D 244 PHE cc_start: 0.7362 (p90) cc_final: 0.7032 (p90) REVERT: D 341 PHE cc_start: 0.6829 (m-10) cc_final: 0.6606 (m-80) REVERT: D 357 MET cc_start: 0.8742 (mtt) cc_final: 0.7984 (mpp) REVERT: D 362 MET cc_start: 0.8975 (mmp) cc_final: 0.8554 (mmt) REVERT: D 379 GLU cc_start: 0.7853 (pm20) cc_final: 0.7300 (pp20) REVERT: D 502 LYS cc_start: 0.7428 (tmtt) cc_final: 0.7080 (mmmt) REVERT: D 669 PHE cc_start: 0.5518 (m-10) cc_final: 0.5279 (m-10) REVERT: D 721 ARG cc_start: 0.6630 (mtp180) cc_final: 0.5554 (tpm170) REVERT: C 132 MET cc_start: 0.8717 (tmm) cc_final: 0.7999 (tmm) REVERT: C 147 ARG cc_start: 0.6350 (mtp85) cc_final: 0.5897 (mtp85) REVERT: C 283 MET cc_start: 0.8535 (mmm) cc_final: 0.8187 (mmm) REVERT: C 290 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8215 (mtt-85) REVERT: C 296 ASN cc_start: 0.8303 (m-40) cc_final: 0.8044 (m-40) REVERT: C 323 SER cc_start: 0.8400 (p) cc_final: 0.8064 (t) REVERT: J 84 PHE cc_start: 0.3775 (m-80) cc_final: 0.2525 (m-10) REVERT: J 218 ASP cc_start: 0.7652 (m-30) cc_final: 0.6681 (p0) REVERT: J 239 ASP cc_start: 0.7232 (t0) cc_final: 0.6627 (p0) REVERT: J 357 MET cc_start: 0.8188 (mtt) cc_final: 0.7148 (mtm) REVERT: J 433 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8125 (tm-30) REVERT: J 545 ASP cc_start: 0.7352 (p0) cc_final: 0.7105 (p0) REVERT: J 563 PHE cc_start: 0.7376 (t80) cc_final: 0.7087 (t80) outliers start: 4 outliers final: 1 residues processed: 642 average time/residue: 0.1701 time to fit residues: 173.8977 Evaluate side-chains 465 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 463 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 265 optimal weight: 2.9990 chunk 194 optimal weight: 50.0000 chunk 139 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 346 optimal weight: 0.0570 chunk 289 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 ASN ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN ** D 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 ASN J 222 GLN J 491 HIS ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.140914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113017 restraints weight = 75992.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111727 restraints weight = 79794.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112703 restraints weight = 65301.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112961 restraints weight = 46277.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113039 restraints weight = 45565.367| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28985 Z= 0.209 Angle : 0.785 13.975 39108 Z= 0.404 Chirality : 0.049 0.269 4290 Planarity : 0.007 0.180 5058 Dihedral : 6.584 65.160 3867 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 3526 helix: 0.71 (0.13), residues: 1544 sheet: -0.90 (0.27), residues: 366 loop : -1.89 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 369 TYR 0.043 0.002 TYR O 60 PHE 0.045 0.002 PHE G 669 TRP 0.042 0.003 TRP B 356 HIS 0.011 0.002 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00466 (28978) covalent geometry : angle 0.78548 (39108) hydrogen bonds : bond 0.05001 ( 1365) hydrogen bonds : angle 5.25294 ( 3852) Misc. bond : bond 0.00332 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 620 time to evaluate : 1.269 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 47 MET cc_start: 0.6602 (ptp) cc_final: 0.6292 (tpp) REVERT: B 148 THR cc_start: 0.8998 (t) cc_final: 0.8639 (m) REVERT: B 227 MET cc_start: 0.8289 (tpt) cc_final: 0.7911 (tpp) REVERT: B 283 MET cc_start: 0.9062 (mmm) cc_final: 0.8602 (mmt) REVERT: B 325 MET cc_start: 0.7968 (mmt) cc_final: 0.7595 (mmt) REVERT: B 362 TYR cc_start: 0.8261 (t80) cc_final: 0.7985 (t80) REVERT: B 364 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7288 (mm-30) REVERT: O 68 GLN cc_start: 0.7605 (tm-30) cc_final: 0.6763 (mt0) REVERT: G 90 MET cc_start: 0.6001 (mmt) cc_final: 0.5588 (mmt) REVERT: G 295 PRO cc_start: 0.8432 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8888 (mmpt) cc_final: 0.8602 (mmmm) REVERT: G 528 MET cc_start: 0.8187 (ttt) cc_final: 0.7977 (ttt) REVERT: G 704 ILE cc_start: 0.8551 (mp) cc_final: 0.7975 (mp) REVERT: G 707 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8111 (ptpp) REVERT: G 770 LEU cc_start: 0.2223 (mt) cc_final: 0.1974 (mt) REVERT: P 68 GLN cc_start: 0.8280 (mt0) cc_final: 0.7793 (mp10) REVERT: P 127 MET cc_start: 0.5193 (ptt) cc_final: 0.4610 (ptt) REVERT: P 139 GLU cc_start: 0.7570 (pt0) cc_final: 0.6896 (tp30) REVERT: P 141 MET cc_start: 0.7902 (mmm) cc_final: 0.7339 (mmm) REVERT: A 81 ASP cc_start: 0.7863 (m-30) cc_final: 0.7660 (m-30) REVERT: A 244 ASP cc_start: 0.7558 (m-30) cc_final: 0.6431 (t0) REVERT: A 334 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6439 (mt-10) REVERT: D 189 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7287 (mptt) REVERT: D 244 PHE cc_start: 0.7616 (p90) cc_final: 0.7046 (p90) REVERT: D 341 PHE cc_start: 0.6824 (m-10) cc_final: 0.6568 (m-80) REVERT: D 349 MET cc_start: 0.7587 (mmp) cc_final: 0.7331 (mmt) REVERT: D 357 MET cc_start: 0.8628 (mtt) cc_final: 0.7881 (mpp) REVERT: D 362 MET cc_start: 0.8942 (mmp) cc_final: 0.8517 (mmt) REVERT: D 379 GLU cc_start: 0.7866 (pm20) cc_final: 0.7278 (pp20) REVERT: D 502 LYS cc_start: 0.7456 (tmtt) cc_final: 0.7096 (mmmt) REVERT: D 534 LEU cc_start: 0.8638 (tp) cc_final: 0.8202 (tp) REVERT: D 601 LEU cc_start: 0.8929 (tp) cc_final: 0.8676 (tt) REVERT: D 721 ARG cc_start: 0.6134 (mtp180) cc_final: 0.5554 (tpm170) REVERT: C 115 ASN cc_start: 0.8825 (t0) cc_final: 0.8566 (t0) REVERT: C 147 ARG cc_start: 0.6413 (mtp85) cc_final: 0.5965 (mtp85) REVERT: C 283 MET cc_start: 0.8470 (mmm) cc_final: 0.8135 (mmm) REVERT: C 290 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8239 (mtt-85) REVERT: C 296 ASN cc_start: 0.8283 (m-40) cc_final: 0.7986 (m-40) REVERT: C 323 SER cc_start: 0.8351 (p) cc_final: 0.8011 (t) REVERT: J 357 MET cc_start: 0.8167 (mtt) cc_final: 0.7098 (mtm) REVERT: J 433 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7941 (tm-30) REVERT: J 466 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8282 (mm-30) REVERT: J 563 PHE cc_start: 0.7297 (t80) cc_final: 0.7009 (t80) outliers start: 4 outliers final: 0 residues processed: 623 average time/residue: 0.1974 time to fit residues: 195.4134 Evaluate side-chains 465 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 123 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 341 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 GLN G 104 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN C 12 ASN C 88 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN J 126 ASN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS J 518 GLN ** J 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.138974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110883 restraints weight = 76050.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109823 restraints weight = 76693.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.110907 restraints weight = 68921.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110761 restraints weight = 49108.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110958 restraints weight = 45833.964| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28985 Z= 0.223 Angle : 0.804 11.860 39108 Z= 0.415 Chirality : 0.049 0.312 4290 Planarity : 0.006 0.128 5058 Dihedral : 6.585 63.407 3867 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.95 % Rotamer: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3526 helix: 0.68 (0.13), residues: 1545 sheet: -0.68 (0.28), residues: 342 loop : -2.00 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 125 TYR 0.037 0.002 TYR D 722 PHE 0.029 0.003 PHE G 669 TRP 0.056 0.003 TRP D 438 HIS 0.016 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00506 (28978) covalent geometry : angle 0.80371 (39108) hydrogen bonds : bond 0.05018 ( 1365) hydrogen bonds : angle 5.26523 ( 3852) Misc. bond : bond 0.00487 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 592 time to evaluate : 1.420 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: B 47 MET cc_start: 0.6872 (ptp) cc_final: 0.6569 (tpt) REVERT: B 148 THR cc_start: 0.9130 (t) cc_final: 0.8771 (m) REVERT: B 227 MET cc_start: 0.8479 (tpt) cc_final: 0.7989 (tpp) REVERT: B 283 MET cc_start: 0.9053 (mmm) cc_final: 0.8662 (mmt) REVERT: B 362 TYR cc_start: 0.8340 (t80) cc_final: 0.8011 (t80) REVERT: B 364 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7306 (mm-30) REVERT: O 68 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6618 (mt0) REVERT: O 127 MET cc_start: 0.6507 (tpt) cc_final: 0.5719 (mmm) REVERT: G 174 ILE cc_start: 0.8845 (mp) cc_final: 0.8426 (mt) REVERT: G 295 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8037 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8617 (mmmm) REVERT: G 704 ILE cc_start: 0.8518 (mp) cc_final: 0.7978 (mp) REVERT: G 707 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8073 (ptpp) REVERT: G 770 LEU cc_start: 0.2575 (mt) cc_final: 0.2161 (mt) REVERT: P 68 GLN cc_start: 0.8302 (mt0) cc_final: 0.7778 (mp10) REVERT: P 90 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7607 (mmt180) REVERT: P 127 MET cc_start: 0.5368 (ptt) cc_final: 0.4368 (ptt) REVERT: P 139 GLU cc_start: 0.7631 (pt0) cc_final: 0.7144 (tp30) REVERT: A 179 ASP cc_start: 0.8107 (t0) cc_final: 0.7648 (t0) REVERT: A 244 ASP cc_start: 0.7341 (m-30) cc_final: 0.6308 (t0) REVERT: A 270 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6803 (mt-10) REVERT: A 334 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6599 (mt-10) REVERT: D 162 TYR cc_start: 0.6950 (t80) cc_final: 0.6673 (t80) REVERT: D 189 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7413 (mmtm) REVERT: D 244 PHE cc_start: 0.7500 (p90) cc_final: 0.7290 (p90) REVERT: D 341 PHE cc_start: 0.6965 (m-10) cc_final: 0.6624 (m-80) REVERT: D 357 MET cc_start: 0.8660 (mtt) cc_final: 0.7969 (mpp) REVERT: D 489 PHE cc_start: 0.6762 (t80) cc_final: 0.6060 (t80) REVERT: D 502 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7152 (mmmt) REVERT: D 721 ARG cc_start: 0.6312 (mtp180) cc_final: 0.5597 (tpm170) REVERT: C 205 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7444 (mp0) REVERT: C 283 MET cc_start: 0.8486 (mmm) cc_final: 0.8190 (mmm) REVERT: C 290 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8339 (mtt-85) REVERT: C 323 SER cc_start: 0.8365 (p) cc_final: 0.7996 (t) REVERT: J 239 ASP cc_start: 0.7787 (t0) cc_final: 0.6801 (p0) REVERT: J 357 MET cc_start: 0.8324 (mtt) cc_final: 0.7493 (mtt) REVERT: J 433 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8052 (tm-30) REVERT: J 563 PHE cc_start: 0.7369 (t80) cc_final: 0.7069 (t80) outliers start: 3 outliers final: 0 residues processed: 595 average time/residue: 0.1986 time to fit residues: 187.4990 Evaluate side-chains 456 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 47 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 245 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS J 126 ASN J 251 HIS ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN J 651 HIS ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110390 restraints weight = 75524.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108798 restraints weight = 80438.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109714 restraints weight = 65748.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109932 restraints weight = 48891.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110037 restraints weight = 45351.782| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28985 Z= 0.226 Angle : 0.810 13.261 39108 Z= 0.419 Chirality : 0.049 0.306 4290 Planarity : 0.007 0.266 5058 Dihedral : 6.652 60.830 3867 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.25 % Favored : 91.66 % Rotamer: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3526 helix: 0.56 (0.13), residues: 1541 sheet: -0.74 (0.27), residues: 372 loop : -1.97 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 91 TYR 0.033 0.002 TYR D 722 PHE 0.031 0.002 PHE G 669 TRP 0.070 0.003 TRP C 340 HIS 0.014 0.002 HIS J 668 Details of bonding type rmsd covalent geometry : bond 0.00516 (28978) covalent geometry : angle 0.80963 (39108) hydrogen bonds : bond 0.04981 ( 1365) hydrogen bonds : angle 5.30144 ( 3852) Misc. bond : bond 0.00879 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 588 time to evaluate : 1.176 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: B 82 MET cc_start: 0.7886 (tpt) cc_final: 0.7654 (tpt) REVERT: B 227 MET cc_start: 0.8185 (tpt) cc_final: 0.7890 (tpp) REVERT: B 283 MET cc_start: 0.8978 (mmm) cc_final: 0.8559 (mmt) REVERT: B 325 MET cc_start: 0.7915 (mmt) cc_final: 0.7533 (mmt) REVERT: B 362 TYR cc_start: 0.8378 (t80) cc_final: 0.8069 (t80) REVERT: B 364 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7383 (mm-30) REVERT: O 68 GLN cc_start: 0.7404 (tm-30) cc_final: 0.6591 (mt0) REVERT: G 174 ILE cc_start: 0.8763 (mp) cc_final: 0.8461 (mt) REVERT: G 295 PRO cc_start: 0.8492 (Cg_endo) cc_final: 0.8076 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8942 (mmpt) cc_final: 0.8661 (mmmm) REVERT: G 662 LEU cc_start: 0.8933 (tp) cc_final: 0.8550 (tp) REVERT: G 704 ILE cc_start: 0.8476 (mp) cc_final: 0.7990 (mp) REVERT: G 707 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8058 (ptpp) REVERT: P 68 GLN cc_start: 0.8232 (mt0) cc_final: 0.7674 (mp10) REVERT: P 91 ARG cc_start: 0.7389 (mmm160) cc_final: 0.7017 (mmm160) REVERT: P 127 MET cc_start: 0.5392 (ptt) cc_final: 0.4845 (ptt) REVERT: P 139 GLU cc_start: 0.7744 (pt0) cc_final: 0.7171 (tp30) REVERT: A 244 ASP cc_start: 0.6882 (m-30) cc_final: 0.5848 (t0) REVERT: A 270 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 162 TYR cc_start: 0.7059 (t80) cc_final: 0.6650 (t80) REVERT: D 189 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7494 (mmtm) REVERT: D 244 PHE cc_start: 0.7627 (p90) cc_final: 0.7361 (p90) REVERT: D 341 PHE cc_start: 0.7002 (m-10) cc_final: 0.6555 (m-80) REVERT: D 357 MET cc_start: 0.8699 (mtt) cc_final: 0.7809 (mpp) REVERT: D 499 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8418 (tm-30) REVERT: D 502 LYS cc_start: 0.7580 (tmtt) cc_final: 0.7339 (mmtt) REVERT: D 669 PHE cc_start: 0.5534 (m-10) cc_final: 0.5264 (m-10) REVERT: C 93 GLU cc_start: 0.8128 (mp0) cc_final: 0.7833 (mp0) REVERT: C 180 LEU cc_start: 0.9021 (tp) cc_final: 0.8818 (mt) REVERT: C 205 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7613 (mp0) REVERT: C 276 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7047 (tm-30) REVERT: C 290 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8144 (mtt-85) REVERT: C 323 SER cc_start: 0.8367 (p) cc_final: 0.7936 (t) REVERT: J 339 LEU cc_start: 0.7148 (mt) cc_final: 0.6887 (mt) REVERT: J 357 MET cc_start: 0.8301 (mtt) cc_final: 0.7444 (mtt) REVERT: J 433 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7956 (tm-30) REVERT: J 466 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8281 (mm-30) REVERT: J 512 ASP cc_start: 0.6954 (m-30) cc_final: 0.6703 (t0) REVERT: J 563 PHE cc_start: 0.7347 (t80) cc_final: 0.7073 (t80) outliers start: 3 outliers final: 0 residues processed: 590 average time/residue: 0.1980 time to fit residues: 185.3178 Evaluate side-chains 445 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 133 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110486 restraints weight = 75929.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108613 restraints weight = 87715.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109924 restraints weight = 77910.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109974 restraints weight = 52267.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.110208 restraints weight = 47357.726| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 28985 Z= 0.218 Angle : 0.814 13.175 39108 Z= 0.419 Chirality : 0.049 0.354 4290 Planarity : 0.007 0.246 5058 Dihedral : 6.672 60.479 3867 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.45 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3526 helix: 0.57 (0.13), residues: 1551 sheet: -0.76 (0.27), residues: 372 loop : -1.98 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 369 TYR 0.033 0.002 TYR J 588 PHE 0.040 0.002 PHE G 669 TRP 0.109 0.004 TRP C 340 HIS 0.011 0.002 HIS J 668 Details of bonding type rmsd covalent geometry : bond 0.00504 (28978) covalent geometry : angle 0.81426 (39108) hydrogen bonds : bond 0.04941 ( 1365) hydrogen bonds : angle 5.33037 ( 3852) Misc. bond : bond 0.00777 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.246 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: B 82 MET cc_start: 0.7900 (tpt) cc_final: 0.7478 (tpt) REVERT: B 184 ASP cc_start: 0.8412 (m-30) cc_final: 0.8209 (m-30) REVERT: B 190 MET cc_start: 0.8691 (mmp) cc_final: 0.8406 (mmp) REVERT: B 227 MET cc_start: 0.8201 (tpt) cc_final: 0.7927 (tpp) REVERT: B 283 MET cc_start: 0.8942 (mmm) cc_final: 0.8590 (mmt) REVERT: B 325 MET cc_start: 0.7936 (mmt) cc_final: 0.7473 (mmt) REVERT: B 362 TYR cc_start: 0.8278 (t80) cc_final: 0.7977 (t80) REVERT: B 364 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7280 (mm-30) REVERT: O 68 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6618 (mt0) REVERT: O 124 GLU cc_start: 0.5550 (mm-30) cc_final: 0.4688 (tm-30) REVERT: O 141 MET cc_start: 0.5097 (tpt) cc_final: 0.4813 (tpt) REVERT: G 174 ILE cc_start: 0.8726 (mp) cc_final: 0.8440 (mt) REVERT: G 295 PRO cc_start: 0.8384 (Cg_endo) cc_final: 0.7945 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8680 (mmmm) REVERT: G 616 MET cc_start: 0.7866 (tpt) cc_final: 0.7545 (mmm) REVERT: G 707 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8240 (pttm) REVERT: P 68 GLN cc_start: 0.8134 (mt0) cc_final: 0.7606 (mp10) REVERT: P 139 GLU cc_start: 0.7800 (pt0) cc_final: 0.7174 (tp30) REVERT: P 141 MET cc_start: 0.8307 (mmt) cc_final: 0.7967 (mmm) REVERT: A 244 ASP cc_start: 0.6792 (m-30) cc_final: 0.5752 (t0) REVERT: A 270 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6837 (mt-10) REVERT: D 189 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7423 (mmtm) REVERT: D 244 PHE cc_start: 0.7683 (p90) cc_final: 0.7470 (p90) REVERT: D 341 PHE cc_start: 0.6919 (m-10) cc_final: 0.6593 (m-80) REVERT: D 357 MET cc_start: 0.8658 (mtt) cc_final: 0.7967 (mpp) REVERT: D 362 MET cc_start: 0.8779 (mmp) cc_final: 0.8493 (mmp) REVERT: D 499 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8434 (tm-30) REVERT: D 502 LYS cc_start: 0.7529 (tmtt) cc_final: 0.7241 (mmtt) REVERT: C 89 THR cc_start: 0.8522 (m) cc_final: 0.7832 (m) REVERT: C 93 GLU cc_start: 0.8189 (mp0) cc_final: 0.7846 (mp0) REVERT: C 205 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7638 (mp0) REVERT: C 290 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8205 (mtt-85) REVERT: C 323 SER cc_start: 0.8382 (p) cc_final: 0.7973 (t) REVERT: J 339 LEU cc_start: 0.7074 (mt) cc_final: 0.6811 (mt) REVERT: J 357 MET cc_start: 0.8347 (mtt) cc_final: 0.7449 (mtt) REVERT: J 433 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8047 (tm-30) REVERT: J 563 PHE cc_start: 0.7413 (t80) cc_final: 0.7172 (t80) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.1966 time to fit residues: 182.8035 Evaluate side-chains 444 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 358 HIS ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 276 GLN D 361 ASN D 372 GLN D 486 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.138740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.111254 restraints weight = 76621.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110598 restraints weight = 70406.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111467 restraints weight = 66586.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111483 restraints weight = 46319.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111627 restraints weight = 42872.847| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28985 Z= 0.200 Angle : 0.815 17.144 39108 Z= 0.417 Chirality : 0.049 0.428 4290 Planarity : 0.006 0.133 5058 Dihedral : 6.630 60.036 3867 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.51 % Favored : 91.46 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3526 helix: 0.57 (0.13), residues: 1545 sheet: -0.66 (0.27), residues: 369 loop : -1.92 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 369 TYR 0.036 0.002 TYR J 588 PHE 0.039 0.002 PHE G 669 TRP 0.104 0.004 TRP C 340 HIS 0.026 0.002 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00462 (28978) covalent geometry : angle 0.81484 (39108) hydrogen bonds : bond 0.04873 ( 1365) hydrogen bonds : angle 5.30322 ( 3852) Misc. bond : bond 0.00604 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 1.217 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: B 82 MET cc_start: 0.8203 (tpt) cc_final: 0.7854 (tpt) REVERT: B 227 MET cc_start: 0.8213 (tpt) cc_final: 0.7953 (tpp) REVERT: B 283 MET cc_start: 0.8898 (mmm) cc_final: 0.8673 (mmt) REVERT: B 325 MET cc_start: 0.7965 (mmt) cc_final: 0.7539 (mmt) REVERT: B 334 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 362 TYR cc_start: 0.8279 (t80) cc_final: 0.7910 (t80) REVERT: B 364 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7332 (mm-30) REVERT: O 68 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6763 (mt0) REVERT: O 131 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7383 (tm-30) REVERT: O 141 MET cc_start: 0.5586 (tpt) cc_final: 0.5192 (tpt) REVERT: G 174 ILE cc_start: 0.8900 (mp) cc_final: 0.8539 (mt) REVERT: G 295 PRO cc_start: 0.8416 (Cg_endo) cc_final: 0.8060 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8966 (mmpt) cc_final: 0.8696 (mmmm) REVERT: G 371 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8237 (pm20) REVERT: G 616 MET cc_start: 0.7908 (tpt) cc_final: 0.7554 (mmm) REVERT: G 703 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7944 (ttp-170) REVERT: G 704 ILE cc_start: 0.8523 (mp) cc_final: 0.8302 (mp) REVERT: P 68 GLN cc_start: 0.8248 (mt0) cc_final: 0.7729 (mp10) REVERT: P 139 GLU cc_start: 0.7767 (pt0) cc_final: 0.7262 (tp30) REVERT: P 159 ASP cc_start: 0.7645 (t0) cc_final: 0.7260 (t0) REVERT: A 224 GLU cc_start: 0.7337 (tp30) cc_final: 0.7076 (tp30) REVERT: A 244 ASP cc_start: 0.6655 (m-30) cc_final: 0.5799 (t0) REVERT: A 270 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6915 (mt-10) REVERT: D 244 PHE cc_start: 0.7661 (p90) cc_final: 0.7430 (p90) REVERT: D 341 PHE cc_start: 0.6999 (m-10) cc_final: 0.6663 (m-80) REVERT: D 362 MET cc_start: 0.8886 (mmp) cc_final: 0.8552 (mmp) REVERT: D 499 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8372 (tm-30) REVERT: D 502 LYS cc_start: 0.7547 (tmtt) cc_final: 0.7272 (mmtt) REVERT: C 88 HIS cc_start: 0.8283 (t-90) cc_final: 0.7476 (t70) REVERT: C 93 GLU cc_start: 0.8267 (mp0) cc_final: 0.7827 (mp0) REVERT: C 147 ARG cc_start: 0.6552 (mtp85) cc_final: 0.6074 (mtp85) REVERT: C 205 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7614 (mp0) REVERT: C 290 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8290 (mtt-85) REVERT: J 339 LEU cc_start: 0.7171 (mt) cc_final: 0.6920 (mt) REVERT: J 357 MET cc_start: 0.8297 (mtt) cc_final: 0.7385 (mtt) REVERT: J 362 MET cc_start: 0.8051 (mmm) cc_final: 0.7440 (mtt) REVERT: J 433 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8040 (tm-30) REVERT: J 563 PHE cc_start: 0.7377 (t80) cc_final: 0.7151 (t80) REVERT: J 690 MET cc_start: 0.6709 (ppp) cc_final: 0.6325 (ptp) outliers start: 1 outliers final: 0 residues processed: 595 average time/residue: 0.1961 time to fit residues: 185.4897 Evaluate side-chains 455 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 92 optimal weight: 9.9990 chunk 250 optimal weight: 0.6980 chunk 234 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 307 optimal weight: 7.9990 chunk 195 optimal weight: 0.0570 chunk 320 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 242 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN D 358 HIS D 361 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN J 358 HIS J 597 ASN ** J 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.140670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110441 restraints weight = 75832.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110068 restraints weight = 51849.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110207 restraints weight = 36184.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110462 restraints weight = 34395.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110608 restraints weight = 32038.310| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28985 Z= 0.159 Angle : 0.793 16.700 39108 Z= 0.401 Chirality : 0.049 0.497 4290 Planarity : 0.006 0.134 5058 Dihedral : 6.437 57.730 3867 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.14), residues: 3526 helix: 0.69 (0.13), residues: 1549 sheet: -0.61 (0.27), residues: 372 loop : -1.89 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 369 TYR 0.024 0.002 TYR G 722 PHE 0.036 0.002 PHE D 489 TRP 0.096 0.003 TRP C 340 HIS 0.017 0.001 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00362 (28978) covalent geometry : angle 0.79335 (39108) hydrogen bonds : bond 0.04716 ( 1365) hydrogen bonds : angle 5.19980 ( 3852) Misc. bond : bond 0.00536 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 82 MET cc_start: 0.8090 (tpt) cc_final: 0.7860 (tpt) REVERT: B 227 MET cc_start: 0.8271 (tpt) cc_final: 0.7980 (tpp) REVERT: B 283 MET cc_start: 0.8850 (mmm) cc_final: 0.8587 (mmt) REVERT: B 325 MET cc_start: 0.7866 (mmt) cc_final: 0.7378 (mmt) REVERT: B 362 TYR cc_start: 0.8329 (t80) cc_final: 0.8003 (t80) REVERT: O 68 GLN cc_start: 0.7649 (tm-30) cc_final: 0.6993 (mt0) REVERT: O 94 LEU cc_start: 0.7266 (pp) cc_final: 0.6537 (tp) REVERT: O 169 LEU cc_start: 0.8287 (tp) cc_final: 0.7859 (tp) REVERT: G 295 PRO cc_start: 0.8293 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: G 334 ASN cc_start: 0.8709 (t0) cc_final: 0.8451 (t0) REVERT: G 363 LYS cc_start: 0.9083 (mmpt) cc_final: 0.8788 (mmmm) REVERT: G 371 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8200 (pm20) REVERT: G 616 MET cc_start: 0.7905 (tpt) cc_final: 0.7670 (mmm) REVERT: G 703 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8153 (ttt-90) REVERT: P 68 GLN cc_start: 0.8341 (mt0) cc_final: 0.7745 (mp10) REVERT: P 132 SER cc_start: 0.8194 (m) cc_final: 0.7741 (p) REVERT: P 139 GLU cc_start: 0.7954 (pt0) cc_final: 0.7231 (tp30) REVERT: P 159 ASP cc_start: 0.8109 (t0) cc_final: 0.7642 (t0) REVERT: A 224 GLU cc_start: 0.7239 (tp30) cc_final: 0.6975 (tp30) REVERT: A 244 ASP cc_start: 0.6730 (m-30) cc_final: 0.5881 (t0) REVERT: A 270 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6591 (mt-10) REVERT: A 334 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6356 (mm-30) REVERT: D 244 PHE cc_start: 0.7791 (p90) cc_final: 0.7496 (p90) REVERT: D 296 GLU cc_start: 0.6498 (pp20) cc_final: 0.6227 (pp20) REVERT: D 325 ASP cc_start: 0.7975 (m-30) cc_final: 0.7734 (t0) REVERT: D 341 PHE cc_start: 0.6857 (m-10) cc_final: 0.6475 (m-80) REVERT: D 362 MET cc_start: 0.8952 (mmp) cc_final: 0.8606 (mmp) REVERT: D 456 PHE cc_start: 0.7001 (p90) cc_final: 0.6735 (p90) REVERT: D 499 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 502 LYS cc_start: 0.7878 (tmtt) cc_final: 0.7243 (mmmt) REVERT: D 690 MET cc_start: 0.7797 (ppp) cc_final: 0.6988 (tpt) REVERT: C 88 HIS cc_start: 0.8192 (t-90) cc_final: 0.7960 (t-90) REVERT: C 147 ARG cc_start: 0.6587 (mtp85) cc_final: 0.6065 (mtp85) REVERT: C 205 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7552 (mp0) REVERT: C 283 MET cc_start: 0.8582 (mmm) cc_final: 0.8359 (mmm) REVERT: C 290 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8155 (mtt-85) REVERT: C 323 SER cc_start: 0.8482 (p) cc_final: 0.8096 (t) REVERT: C 352 PHE cc_start: 0.7916 (t80) cc_final: 0.7588 (t80) REVERT: J 169 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7589 (ptt180) REVERT: J 357 MET cc_start: 0.8563 (mtt) cc_final: 0.7626 (mtt) REVERT: J 362 MET cc_start: 0.8057 (mmm) cc_final: 0.7735 (mtt) REVERT: J 433 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8231 (tm-30) REVERT: J 690 MET cc_start: 0.6159 (ppp) cc_final: 0.5945 (ptp) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.1939 time to fit residues: 189.5906 Evaluate side-chains 463 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 81 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 287 optimal weight: 30.0000 chunk 289 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 304 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 GLN ** D 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 173 HIS ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110015 restraints weight = 76203.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108237 restraints weight = 79952.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.109490 restraints weight = 68090.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109439 restraints weight = 51042.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109625 restraints weight = 44635.640| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28985 Z= 0.229 Angle : 0.833 16.270 39108 Z= 0.427 Chirality : 0.050 0.511 4290 Planarity : 0.006 0.138 5058 Dihedral : 6.543 60.293 3867 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3526 helix: 0.57 (0.13), residues: 1561 sheet: -0.62 (0.27), residues: 372 loop : -1.93 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 453 TYR 0.022 0.002 TYR G 422 PHE 0.040 0.003 PHE J 46 TRP 0.104 0.004 TRP C 340 HIS 0.014 0.002 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00527 (28978) covalent geometry : angle 0.83255 (39108) hydrogen bonds : bond 0.04889 ( 1365) hydrogen bonds : angle 5.36572 ( 3852) Misc. bond : bond 0.00681 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5079.39 seconds wall clock time: 89 minutes 4.19 seconds (5344.19 seconds total)