Starting phenix.real_space_refine on Tue Jun 24 09:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x5z_22067/06_2025/6x5z_22067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5z_22067/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6x5z_22067/06_2025/6x5z_22067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5z_22067/06_2025/6x5z_22067.map" model { file = "/net/cci-nas-00/data/ceres_data/6x5z_22067/06_2025/6x5z_22067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5z_22067/06_2025/6x5z_22067.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.98, per 1000 atoms: 0.56 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: 7.28 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.56 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: 11.79 Time building geometry restraints manager: 8.63 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: 0.18 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.150 Check model and map are aligned: 0.190 Set scattering table: 0.300 Process input model: 63.540 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.080 0.004 TRP C 356 HIS 0.014 0.002 HIS D 651 PHE 0.024 0.003 PHE J 540 TYR 0.104 0.003 TYR P 162 ARG 0.020 0.001 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.18954 ( 1365) hydrogen bonds : angle 7.37910 ( 3852) covalent geometry : bond 0.00768 (28978) covalent geometry : angle 1.07213 (39108) 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 : 3.327 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: 0.4329 time to fit residues: 678.4084 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 : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 274 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 0.0270 chunk 204 optimal weight: 8.9990 chunk 317 optimal weight: 2.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.145959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115204 restraints weight = 75538.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114416 restraints weight = 51497.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115393 restraints weight = 38999.373| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3474 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= 0.183 Angle : 0.800 10.190 39108 Z= 0.415 Chirality : 0.048 0.282 4290 Planarity : 0.006 0.082 5058 Dihedral : 6.909 68.917 3867 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.23 % Favored : 92.51 % Rotamer: Outliers : 0.36 % Allowed : 5.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3526 helix: 0.54 (0.12), residues: 1588 sheet: -1.08 (0.27), residues: 369 loop : -2.11 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 356 HIS 0.012 0.002 HIS J 97 PHE 0.031 0.002 PHE G 669 TYR 0.032 0.002 TYR P 60 ARG 0.008 0.001 ARG D 719 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 1365) hydrogen bonds : angle 5.66696 ( 3852) covalent geometry : bond 0.00405 (28978) covalent geometry : angle 0.80000 (39108) Misc. bond : bond 0.00539 ( 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 770 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 759 time to evaluate : 3.474 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: B 132 MET cc_start: 0.8872 (ppp) cc_final: 0.8655 (tmm) REVERT: B 148 THR cc_start: 0.8919 (t) cc_final: 0.8705 (m) REVERT: B 169 TYR cc_start: 0.8156 (m-80) cc_final: 0.7793 (m-10) REVERT: B 184 ASP cc_start: 0.8214 (m-30) cc_final: 0.7790 (m-30) REVERT: B 279 TYR cc_start: 0.8529 (t80) cc_final: 0.8275 (t80) REVERT: B 283 MET cc_start: 0.8939 (mmm) cc_final: 0.8434 (mmt) REVERT: B 290 ARG cc_start: 0.8840 (mtt180) cc_final: 0.8397 (mtt90) REVERT: B 334 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6017 (mt-10) REVERT: B 364 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7191 (mm-30) REVERT: O 189 LYS cc_start: 0.8012 (pttp) cc_final: 0.7794 (pttp) REVERT: O 198 LYS cc_start: 0.7943 (tttt) cc_final: 0.7687 (mmtt) REVERT: G 42 ASP cc_start: 0.7604 (t0) cc_final: 0.7399 (t0) REVERT: G 90 MET cc_start: 0.6253 (mmt) cc_final: 0.5836 (mmm) REVERT: G 98 GLU cc_start: 0.5996 (tt0) cc_final: 0.5428 (tt0) REVERT: G 116 THR cc_start: 0.8246 (m) cc_final: 0.7726 (t) REVERT: G 126 ASN cc_start: 0.8137 (m-40) cc_final: 0.7707 (m-40) REVERT: G 295 PRO cc_start: 0.8415 (Cg_endo) cc_final: 0.8001 (Cg_exo) REVERT: G 473 PHE cc_start: 0.8720 (t80) cc_final: 0.8441 (t80) REVERT: G 488 PHE cc_start: 0.7928 (t80) cc_final: 0.7698 (t80) REVERT: P 136 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8632 (mtpt) REVERT: A 120 THR cc_start: 0.8886 (t) cc_final: 0.8392 (t) REVERT: A 205 GLU cc_start: 0.7203 (pt0) cc_final: 0.6703 (mt-10) REVERT: A 211 ASP cc_start: 0.6644 (m-30) cc_final: 0.6344 (m-30) REVERT: A 225 ASN cc_start: 0.7785 (m110) cc_final: 0.7398 (m110) REVERT: A 244 ASP cc_start: 0.8222 (m-30) cc_final: 0.6999 (t0) REVERT: A 270 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 290 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7919 (mtt90) REVERT: A 334 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6284 (mm-30) REVERT: D 189 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7506 (mmtm) REVERT: D 244 PHE cc_start: 0.7459 (p90) cc_final: 0.6706 (p90) REVERT: D 362 MET cc_start: 0.8899 (mmp) cc_final: 0.8593 (mmm) REVERT: D 379 GLU cc_start: 0.7684 (pm20) cc_final: 0.7216 (pp20) REVERT: D 403 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7347 (mtp180) REVERT: D 435 MET cc_start: 0.7642 (ttt) cc_final: 0.7019 (ttp) REVERT: D 534 LEU cc_start: 0.8321 (tp) cc_final: 0.7925 (tp) REVERT: D 547 THR cc_start: 0.8480 (p) cc_final: 0.8102 (t) REVERT: D 703 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7067 (tpt90) REVERT: D 776 MET cc_start: 0.6001 (mpp) cc_final: 0.5770 (mpp) REVERT: C 47 MET cc_start: 0.7938 (ptp) cc_final: 0.7663 (ptp) REVERT: C 87 HIS cc_start: 0.8204 (t70) cc_final: 0.7953 (t-90) REVERT: C 147 ARG cc_start: 0.6614 (mtp85) cc_final: 0.6068 (mtp85) REVERT: C 296 ASN cc_start: 0.8395 (m-40) cc_final: 0.7818 (m-40) REVERT: C 323 SER cc_start: 0.8520 (p) cc_final: 0.8248 (t) REVERT: J 218 ASP cc_start: 0.7895 (m-30) cc_final: 0.6970 (p0) REVERT: J 239 ASP cc_start: 0.6731 (p0) cc_final: 0.6332 (p0) REVERT: J 390 LEU cc_start: 0.8181 (tt) cc_final: 0.7657 (tt) REVERT: J 433 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8280 (tm-30) REVERT: J 563 PHE cc_start: 0.7650 (t80) cc_final: 0.7305 (t80) REVERT: J 612 SER cc_start: 0.5442 (m) cc_final: 0.4612 (p) outliers start: 11 outliers final: 2 residues processed: 767 average time/residue: 0.4001 time to fit residues: 485.9180 Evaluate side-chains 524 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 522 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 140 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 293 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 275 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 overall best weight: 3.3502 ------------------------------------------------------------------------------- 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 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN G 490 ASN ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 661 ASN G 726 ASN ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 314 GLN D 78 GLN ** 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 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 = 0.4054 r_free = 0.4054 target = 0.143261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114982 restraints weight = 75315.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113799 restraints weight = 79665.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.115123 restraints weight = 66756.850| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28985 Z= 0.204 Angle : 0.778 10.634 39108 Z= 0.402 Chirality : 0.048 0.261 4290 Planarity : 0.006 0.124 5058 Dihedral : 6.684 64.607 3867 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3526 helix: 0.76 (0.13), residues: 1566 sheet: -0.83 (0.28), residues: 360 loop : -2.10 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 340 HIS 0.009 0.002 HIS P 153 PHE 0.045 0.003 PHE G 669 TYR 0.046 0.002 TYR J 722 ARG 0.013 0.001 ARG O 178 Details of bonding type rmsd hydrogen bonds : bond 0.05253 ( 1365) hydrogen bonds : angle 5.44696 ( 3852) covalent geometry : bond 0.00461 (28978) covalent geometry : angle 0.77846 (39108) Misc. bond : bond 0.00219 ( 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 678 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 673 time to evaluate : 3.238 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 148 THR cc_start: 0.9052 (t) cc_final: 0.8717 (m) REVERT: B 184 ASP cc_start: 0.7942 (m-30) cc_final: 0.7582 (m-30) REVERT: B 227 MET cc_start: 0.8104 (tpt) cc_final: 0.7891 (tpp) REVERT: B 283 MET cc_start: 0.9037 (mmm) cc_final: 0.8670 (mmt) REVERT: B 290 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8343 (mtt90) REVERT: B 364 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7083 (mm-30) REVERT: O 68 GLN cc_start: 0.7600 (tm-30) cc_final: 0.6919 (mt0) REVERT: O 141 MET cc_start: 0.5643 (tpt) cc_final: 0.4706 (tpp) REVERT: G 90 MET cc_start: 0.6213 (mmt) cc_final: 0.5792 (mmm) REVERT: G 98 GLU cc_start: 0.6112 (tt0) cc_final: 0.5114 (tt0) REVERT: G 126 ASN cc_start: 0.8103 (m-40) cc_final: 0.7739 (m-40) REVERT: G 174 ILE cc_start: 0.8754 (mp) cc_final: 0.8424 (mt) REVERT: G 238 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.6765 (p0) REVERT: G 244 PHE cc_start: 0.8776 (p90) cc_final: 0.8104 (p90) REVERT: G 295 PRO cc_start: 0.8452 (Cg_endo) cc_final: 0.8033 (Cg_exo) REVERT: P 139 GLU cc_start: 0.7335 (pt0) cc_final: 0.6876 (tp30) REVERT: A 81 ASP cc_start: 0.8004 (m-30) cc_final: 0.7788 (m-30) REVERT: A 179 ASP cc_start: 0.8147 (t0) cc_final: 0.7831 (t0) REVERT: A 205 GLU cc_start: 0.7065 (pt0) cc_final: 0.6808 (mt-10) REVERT: A 211 ASP cc_start: 0.6334 (m-30) cc_final: 0.6127 (m-30) REVERT: A 244 ASP cc_start: 0.8066 (m-30) cc_final: 0.6626 (t0) REVERT: A 270 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 325 MET cc_start: 0.8575 (mmp) cc_final: 0.8265 (mmp) REVERT: D 175 LEU cc_start: 0.6901 (mp) cc_final: 0.6550 (tt) REVERT: D 189 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7409 (mmtm) REVERT: D 244 PHE cc_start: 0.7593 (p90) cc_final: 0.6848 (p90) REVERT: D 346 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8022 (tttp) REVERT: D 362 MET cc_start: 0.8931 (mmp) cc_final: 0.8511 (mmt) REVERT: D 379 GLU cc_start: 0.7803 (pm20) cc_final: 0.7259 (pp20) REVERT: D 435 MET cc_start: 0.7474 (ttt) cc_final: 0.6534 (ttp) REVERT: D 502 LYS cc_start: 0.7309 (tmtt) cc_final: 0.7105 (mmmt) REVERT: D 534 LEU cc_start: 0.8441 (tp) cc_final: 0.8159 (tp) REVERT: D 547 THR cc_start: 0.8466 (p) cc_final: 0.8037 (t) REVERT: D 703 ARG cc_start: 0.7566 (tpt90) cc_final: 0.7020 (tpt90) REVERT: C 137 GLN cc_start: 0.7914 (mm110) cc_final: 0.7686 (mm110) REVERT: C 147 ARG cc_start: 0.6397 (mtp85) cc_final: 0.5931 (mtp85) REVERT: C 205 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7329 (mp0) REVERT: C 293 LEU cc_start: 0.8855 (mt) cc_final: 0.8550 (mt) REVERT: C 313 MET cc_start: 0.8956 (mmm) cc_final: 0.8507 (mmm) REVERT: C 323 SER cc_start: 0.8398 (p) cc_final: 0.8084 (t) REVERT: J 84 PHE cc_start: 0.4065 (m-10) cc_final: 0.2969 (m-80) REVERT: J 218 ASP cc_start: 0.7568 (m-30) cc_final: 0.6738 (p0) REVERT: J 357 MET cc_start: 0.8310 (mtt) cc_final: 0.7689 (mtt) REVERT: J 433 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8131 (tm-30) REVERT: J 563 PHE cc_start: 0.7299 (t80) cc_final: 0.6941 (t80) outliers start: 5 outliers final: 0 residues processed: 675 average time/residue: 0.4017 time to fit residues: 426.9122 Evaluate side-chains 493 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 340 optimal weight: 7.9990 chunk 322 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 275 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN G 153 HIS ** 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 444 ASN G 479 ASN ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 92 ASN A 225 ASN A 314 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 HIS C 296 ASN C 314 GLN C 371 HIS J 126 ASN J 240 ASN J 491 HIS ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.145292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.116980 restraints weight = 76805.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.116236 restraints weight = 80643.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.117433 restraints weight = 65205.871| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28985 Z= 0.160 Angle : 0.743 10.198 39108 Z= 0.381 Chirality : 0.047 0.239 4290 Planarity : 0.006 0.116 5058 Dihedral : 6.503 63.658 3867 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.48 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3526 helix: 0.86 (0.13), residues: 1557 sheet: -0.82 (0.28), residues: 360 loop : -2.02 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 340 HIS 0.011 0.001 HIS D 492 PHE 0.045 0.002 PHE G 669 TYR 0.037 0.002 TYR J 287 ARG 0.008 0.001 ARG O 125 Details of bonding type rmsd hydrogen bonds : bond 0.04964 ( 1365) hydrogen bonds : angle 5.22695 ( 3852) covalent geometry : bond 0.00344 (28978) covalent geometry : angle 0.74335 (39108) Misc. bond : bond 0.00195 ( 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 690 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 687 time to evaluate : 3.204 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: B 47 MET cc_start: 0.7813 (ptp) cc_final: 0.6707 (tpt) REVERT: B 54 VAL cc_start: 0.9569 (t) cc_final: 0.9347 (m) REVERT: B 148 THR cc_start: 0.9044 (t) cc_final: 0.8621 (m) REVERT: B 190 MET cc_start: 0.8484 (mmt) cc_final: 0.8099 (mmp) REVERT: B 283 MET cc_start: 0.9073 (mmm) cc_final: 0.8629 (mmt) REVERT: B 290 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8151 (mtt90) REVERT: B 364 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7166 (mm-30) REVERT: O 68 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6734 (mt0) REVERT: O 124 GLU cc_start: 0.4319 (mm-30) cc_final: 0.3926 (tm-30) REVERT: O 127 MET cc_start: 0.6207 (tpt) cc_final: 0.5699 (mtp) REVERT: O 141 MET cc_start: 0.5991 (tpt) cc_final: 0.5746 (tpt) REVERT: G 90 MET cc_start: 0.5750 (mmt) cc_final: 0.5339 (mmm) REVERT: G 98 GLU cc_start: 0.5869 (tt0) cc_final: 0.5618 (tt0) REVERT: G 116 THR cc_start: 0.8054 (m) cc_final: 0.7652 (t) REVERT: G 126 ASN cc_start: 0.8004 (m-40) cc_final: 0.7626 (m-40) REVERT: G 295 PRO cc_start: 0.8390 (Cg_endo) cc_final: 0.7985 (Cg_exo) REVERT: G 371 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8124 (pm20) REVERT: G 515 MET cc_start: 0.8290 (mpp) cc_final: 0.7973 (mpp) REVERT: G 662 LEU cc_start: 0.8918 (tp) cc_final: 0.8636 (tp) REVERT: G 704 ILE cc_start: 0.8479 (mp) cc_final: 0.8270 (mp) REVERT: P 127 MET cc_start: 0.5242 (ptt) cc_final: 0.4857 (ptt) REVERT: P 139 GLU cc_start: 0.7541 (pt0) cc_final: 0.7061 (tp30) REVERT: P 141 MET cc_start: 0.8381 (mmt) cc_final: 0.7800 (mmm) REVERT: A 179 ASP cc_start: 0.8179 (t0) cc_final: 0.7756 (t0) REVERT: A 205 GLU cc_start: 0.7089 (pt0) cc_final: 0.6857 (mt-10) REVERT: A 211 ASP cc_start: 0.6504 (m-30) cc_final: 0.6298 (m-30) REVERT: A 244 ASP cc_start: 0.7755 (m-30) cc_final: 0.6625 (t0) REVERT: A 270 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6751 (mt-10) REVERT: A 325 MET cc_start: 0.8604 (mmp) cc_final: 0.8318 (mmp) REVERT: A 352 PHE cc_start: 0.8637 (t80) cc_final: 0.8361 (t80) REVERT: D 189 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7322 (mmtm) REVERT: D 244 PHE cc_start: 0.7470 (p90) cc_final: 0.6798 (p90) REVERT: D 357 MET cc_start: 0.8578 (mtt) cc_final: 0.7831 (mpp) REVERT: D 362 MET cc_start: 0.8927 (mmp) cc_final: 0.8466 (mmt) REVERT: D 369 ARG cc_start: 0.6885 (mtt180) cc_final: 0.6663 (tpt-90) REVERT: D 379 GLU cc_start: 0.7729 (pm20) cc_final: 0.7222 (pp20) REVERT: D 435 MET cc_start: 0.7161 (ttt) cc_final: 0.6711 (ttp) REVERT: D 489 PHE cc_start: 0.6727 (t80) cc_final: 0.5862 (t80) REVERT: D 534 LEU cc_start: 0.8480 (tp) cc_final: 0.8160 (tp) REVERT: D 721 ARG cc_start: 0.6696 (mtp180) cc_final: 0.5514 (tpm170) REVERT: D 739 ARG cc_start: 0.5879 (mpp-170) cc_final: 0.5618 (mmp80) REVERT: C 147 ARG cc_start: 0.6381 (mtp85) cc_final: 0.6064 (mtp180) REVERT: C 283 MET cc_start: 0.8557 (mmm) cc_final: 0.8288 (mmm) REVERT: C 290 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7865 (mtt-85) REVERT: C 293 LEU cc_start: 0.8789 (mt) cc_final: 0.8464 (mt) REVERT: C 323 SER cc_start: 0.8352 (p) cc_final: 0.8013 (t) REVERT: J 90 MET cc_start: 0.5719 (mmm) cc_final: 0.5314 (mmm) REVERT: J 218 ASP cc_start: 0.7564 (m-30) cc_final: 0.6693 (p0) REVERT: J 239 ASP cc_start: 0.7073 (t0) cc_final: 0.6500 (p0) REVERT: J 357 MET cc_start: 0.8041 (mtt) cc_final: 0.7188 (mtt) REVERT: J 433 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8021 (tm-30) REVERT: J 563 PHE cc_start: 0.7265 (t80) cc_final: 0.6880 (t80) outliers start: 3 outliers final: 0 residues processed: 688 average time/residue: 0.4022 time to fit residues: 438.0015 Evaluate side-chains 506 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 323 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 338 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN ** 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 661 ASN ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 HIS C 88 HIS ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS C 296 ASN J 126 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS J 651 HIS ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.137885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110026 restraints weight = 76654.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108900 restraints weight = 76102.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109847 restraints weight = 69240.214| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 28985 Z= 0.289 Angle : 0.880 11.361 39108 Z= 0.457 Chirality : 0.052 0.288 4290 Planarity : 0.007 0.160 5058 Dihedral : 6.779 62.925 3867 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.25 % Favored : 91.66 % Rotamer: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3526 helix: 0.49 (0.13), residues: 1542 sheet: -0.95 (0.27), residues: 366 loop : -1.99 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP B 356 HIS 0.019 0.002 HIS C 88 PHE 0.028 0.003 PHE A 90 TYR 0.047 0.003 TYR O 60 ARG 0.034 0.001 ARG O 125 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 1365) hydrogen bonds : angle 5.42597 ( 3852) covalent geometry : bond 0.00655 (28978) covalent geometry : angle 0.88024 (39108) Misc. bond : bond 0.00542 ( 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 612 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 609 time to evaluate : 4.211 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 142 LEU cc_start: 0.9239 (mt) cc_final: 0.8997 (mt) REVERT: B 227 MET cc_start: 0.8424 (tpt) cc_final: 0.8123 (tpp) REVERT: B 283 MET cc_start: 0.9211 (mmm) cc_final: 0.8793 (mmt) REVERT: B 362 TYR cc_start: 0.8362 (t80) cc_final: 0.8006 (t80) REVERT: B 364 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7459 (mm-30) REVERT: O 124 GLU cc_start: 0.5263 (mm-30) cc_final: 0.4626 (tm-30) REVERT: O 127 MET cc_start: 0.6197 (tpt) cc_final: 0.5911 (mpp) REVERT: G 90 MET cc_start: 0.6017 (mmt) cc_final: 0.5645 (mmt) REVERT: G 295 PRO cc_start: 0.8518 (Cg_endo) cc_final: 0.8061 (Cg_exo) REVERT: G 413 LYS cc_start: 0.7654 (mttt) cc_final: 0.7403 (mmtp) REVERT: G 707 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8107 (ptpp) REVERT: P 68 GLN cc_start: 0.8321 (mt0) cc_final: 0.7801 (mp10) REVERT: A 205 GLU cc_start: 0.7336 (pt0) cc_final: 0.7124 (mt-10) REVERT: A 244 ASP cc_start: 0.7486 (m-30) cc_final: 0.6438 (t0) REVERT: A 270 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6742 (mt-10) REVERT: D 189 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7381 (mmtm) REVERT: D 244 PHE cc_start: 0.7657 (p90) cc_final: 0.7053 (p90) REVERT: D 346 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8016 (tttp) REVERT: D 362 MET cc_start: 0.8957 (mmp) cc_final: 0.8584 (mmt) REVERT: D 379 GLU cc_start: 0.7962 (pm20) cc_final: 0.7328 (pp20) REVERT: D 669 PHE cc_start: 0.5548 (m-10) cc_final: 0.5338 (m-10) REVERT: D 721 ARG cc_start: 0.6247 (mtp180) cc_final: 0.5561 (tpm170) REVERT: C 132 MET cc_start: 0.8722 (tmm) cc_final: 0.8231 (tmm) REVERT: C 323 SER cc_start: 0.8469 (p) cc_final: 0.8105 (t) REVERT: J 43 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7377 (tmtt) REVERT: J 90 MET cc_start: 0.5554 (mmm) cc_final: 0.5326 (mmm) REVERT: J 357 MET cc_start: 0.8212 (mtt) cc_final: 0.7192 (mtm) REVERT: J 433 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8132 (tm-30) REVERT: J 466 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8290 (mm-30) REVERT: J 545 ASP cc_start: 0.7559 (p0) cc_final: 0.7241 (p0) REVERT: J 563 PHE cc_start: 0.7315 (t80) cc_final: 0.7074 (t80) REVERT: J 588 TYR cc_start: 0.5963 (m-80) cc_final: 0.5391 (m-80) REVERT: J 651 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8022 (t-90) outliers start: 3 outliers final: 0 residues processed: 612 average time/residue: 0.5948 time to fit residues: 585.4001 Evaluate side-chains 460 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 319 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 0.0870 chunk 132 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 314 GLN ** D 276 GLN ** 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 372 GLN D 415 GLN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN C 88 HIS ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 314 GLN J 126 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS ** J 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.142327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114159 restraints weight = 76476.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113417 restraints weight = 77325.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114787 restraints weight = 62057.106| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 28985 Z= 0.162 Angle : 0.769 14.050 39108 Z= 0.394 Chirality : 0.048 0.250 4290 Planarity : 0.008 0.446 5058 Dihedral : 6.681 101.822 3867 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.48 % Rotamer: Outliers : 0.13 % Allowed : 2.87 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3526 helix: 0.79 (0.13), residues: 1541 sheet: -0.87 (0.27), residues: 366 loop : -1.87 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 356 HIS 0.013 0.001 HIS D 492 PHE 0.032 0.002 PHE G 669 TYR 0.039 0.002 TYR D 722 ARG 0.030 0.001 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 1365) hydrogen bonds : angle 5.12015 ( 3852) covalent geometry : bond 0.00361 (28978) covalent geometry : angle 0.76882 (39108) Misc. bond : bond 0.00738 ( 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 652 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 648 time to evaluate : 3.408 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 190 MET cc_start: 0.8538 (mmt) cc_final: 0.8290 (mmm) REVERT: B 227 MET cc_start: 0.8515 (tpt) cc_final: 0.8188 (tpp) REVERT: B 290 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8120 (mtt90) REVERT: B 325 MET cc_start: 0.7922 (mmt) cc_final: 0.7572 (mmt) REVERT: B 362 TYR cc_start: 0.8296 (t80) cc_final: 0.8023 (t80) REVERT: B 364 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7230 (mm-30) REVERT: O 124 GLU cc_start: 0.5427 (mm-30) cc_final: 0.4889 (tm-30) REVERT: G 98 GLU cc_start: 0.5861 (tt0) cc_final: 0.5137 (tt0) REVERT: G 269 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7127 (mm-30) REVERT: G 295 PRO cc_start: 0.8411 (Cg_endo) cc_final: 0.7997 (Cg_exo) REVERT: G 371 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8177 (pm20) REVERT: G 388 MET cc_start: 0.8635 (mpp) cc_final: 0.8239 (mpp) REVERT: G 617 LEU cc_start: 0.7567 (pp) cc_final: 0.5526 (pp) REVERT: G 707 LYS cc_start: 0.8472 (ptpp) cc_final: 0.7959 (ptpp) REVERT: G 770 LEU cc_start: 0.2608 (mt) cc_final: 0.2173 (mt) REVERT: P 68 GLN cc_start: 0.8314 (mt0) cc_final: 0.7788 (mp10) REVERT: P 127 MET cc_start: 0.5428 (ptt) cc_final: 0.5089 (ptt) REVERT: A 81 ASP cc_start: 0.7776 (m-30) cc_final: 0.7552 (m-30) REVERT: A 120 THR cc_start: 0.8765 (t) cc_final: 0.8561 (t) REVERT: A 179 ASP cc_start: 0.8081 (t0) cc_final: 0.7547 (t0) REVERT: A 205 GLU cc_start: 0.7268 (pt0) cc_final: 0.6737 (mt-10) REVERT: A 225 ASN cc_start: 0.7582 (m110) cc_final: 0.7271 (m110) REVERT: A 244 ASP cc_start: 0.7540 (m-30) cc_final: 0.6422 (t0) REVERT: A 270 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 334 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6558 (mm-30) REVERT: D 189 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7347 (mptt) REVERT: D 244 PHE cc_start: 0.7422 (p90) cc_final: 0.6978 (p90) REVERT: D 296 GLU cc_start: 0.6359 (pp20) cc_final: 0.6148 (pp20) REVERT: D 362 MET cc_start: 0.8994 (mmp) cc_final: 0.8498 (mmt) REVERT: D 499 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 502 LYS cc_start: 0.7441 (tmtt) cc_final: 0.7147 (mmmt) REVERT: D 534 LEU cc_start: 0.8606 (tp) cc_final: 0.8385 (tp) REVERT: D 721 ARG cc_start: 0.6292 (mtp180) cc_final: 0.5600 (tpm170) REVERT: C 44 MET cc_start: 0.8531 (ttm) cc_final: 0.8316 (tpp) REVERT: C 88 HIS cc_start: 0.8090 (t70) cc_final: 0.7625 (t-90) REVERT: C 93 GLU cc_start: 0.7888 (mp0) cc_final: 0.7630 (mp0) REVERT: C 132 MET cc_start: 0.8624 (tmm) cc_final: 0.7845 (tmm) REVERT: C 212 ILE cc_start: 0.8403 (tt) cc_final: 0.8191 (tt) REVERT: C 214 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8120 (mt-10) REVERT: C 323 SER cc_start: 0.8474 (p) cc_final: 0.8127 (t) REVERT: J 43 LYS cc_start: 0.7705 (tmtt) cc_final: 0.7464 (tmtt) REVERT: J 239 ASP cc_start: 0.7785 (t0) cc_final: 0.6775 (p0) REVERT: J 357 MET cc_start: 0.8189 (mtt) cc_final: 0.7359 (mtt) REVERT: J 370 GLU cc_start: 0.6889 (pm20) cc_final: 0.5847 (tm-30) REVERT: J 433 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8020 (tm-30) REVERT: J 466 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8193 (mm-30) REVERT: J 563 PHE cc_start: 0.7344 (t80) cc_final: 0.7045 (t80) outliers start: 4 outliers final: 1 residues processed: 651 average time/residue: 0.3843 time to fit residues: 399.6820 Evaluate side-chains 492 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 348 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 342 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN D 415 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 137 GLN C 173 HIS C 263 GLN J 222 GLN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111115 restraints weight = 76387.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110037 restraints weight = 79136.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.110983 restraints weight = 63275.438| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 28985 Z= 0.231 Angle : 0.808 11.824 39108 Z= 0.419 Chirality : 0.049 0.292 4290 Planarity : 0.006 0.144 5058 Dihedral : 6.533 60.517 3867 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.28 % Favored : 91.69 % Rotamer: Outliers : 0.03 % Allowed : 1.89 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3526 helix: 0.66 (0.13), residues: 1548 sheet: -0.55 (0.28), residues: 339 loop : -1.94 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP C 340 HIS 0.024 0.002 HIS D 251 PHE 0.046 0.003 PHE G 621 TYR 0.031 0.002 TYR D 722 ARG 0.017 0.001 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 1365) hydrogen bonds : angle 5.27521 ( 3852) covalent geometry : bond 0.00525 (28978) covalent geometry : angle 0.80835 (39108) Misc. bond : bond 0.00929 ( 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 605 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 604 time to evaluate : 3.270 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: B 82 MET cc_start: 0.8207 (tpt) cc_final: 0.7827 (tpt) REVERT: B 227 MET cc_start: 0.8487 (tpt) cc_final: 0.8111 (tpp) REVERT: B 362 TYR cc_start: 0.8340 (t80) cc_final: 0.8014 (t80) REVERT: B 364 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7302 (mm-30) REVERT: G 98 GLU cc_start: 0.5898 (tt0) cc_final: 0.5484 (tt0) REVERT: G 277 LEU cc_start: 0.7394 (tp) cc_final: 0.7138 (tt) REVERT: G 295 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8044 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8583 (mmmm) REVERT: G 707 LYS cc_start: 0.8481 (ptpp) cc_final: 0.7942 (ptpp) REVERT: G 770 LEU cc_start: 0.2497 (mt) cc_final: 0.1959 (mt) REVERT: P 68 GLN cc_start: 0.8302 (mt0) cc_final: 0.7767 (mp10) REVERT: P 141 MET cc_start: 0.8317 (mmp) cc_final: 0.8062 (mmm) REVERT: P 159 ASP cc_start: 0.7708 (t0) cc_final: 0.7284 (t0) REVERT: A 179 ASP cc_start: 0.8223 (t0) cc_final: 0.7710 (t0) REVERT: A 205 GLU cc_start: 0.7477 (pt0) cc_final: 0.7123 (mt-10) REVERT: A 244 ASP cc_start: 0.7122 (m-30) cc_final: 0.6052 (t0) REVERT: A 270 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6750 (mt-10) REVERT: A 355 MET cc_start: 0.8653 (mmp) cc_final: 0.8402 (tpp) REVERT: D 162 TYR cc_start: 0.7020 (t80) cc_final: 0.6685 (t80) REVERT: D 346 LYS cc_start: 0.8504 (tmtt) cc_final: 0.7984 (tttp) REVERT: D 362 MET cc_start: 0.8922 (mmp) cc_final: 0.8484 (mmt) REVERT: D 418 GLN cc_start: 0.8067 (tp40) cc_final: 0.7741 (tp40) REVERT: D 499 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8411 (tm-30) REVERT: D 502 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7321 (mmtt) REVERT: D 522 ASP cc_start: 0.8278 (m-30) cc_final: 0.7519 (p0) REVERT: C 132 MET cc_start: 0.8763 (tmm) cc_final: 0.8018 (tmm) REVERT: C 205 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7435 (mp0) REVERT: C 290 ARG cc_start: 0.8837 (mpt-90) cc_final: 0.8511 (mpt-90) REVERT: C 323 SER cc_start: 0.8389 (p) cc_final: 0.8017 (t) REVERT: J 43 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7284 (tmtt) REVERT: J 45 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6961 (mm-30) REVERT: J 357 MET cc_start: 0.8240 (mtt) cc_final: 0.7408 (mtt) REVERT: J 370 GLU cc_start: 0.6743 (pm20) cc_final: 0.5723 (tm-30) REVERT: J 433 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8046 (tm-30) REVERT: J 466 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8190 (mm-30) REVERT: J 563 PHE cc_start: 0.7373 (t80) cc_final: 0.7100 (t80) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.3935 time to fit residues: 378.7235 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 : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 1 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 289 optimal weight: 0.9980 chunk 337 optimal weight: 0.4980 chunk 247 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 198 optimal weight: 0.0060 overall best weight: 2.5000 ------------------------------------------------------------------------------- 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 358 HIS ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 HIS A 314 GLN ** D 153 HIS ** 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 372 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.140561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112569 restraints weight = 76451.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111828 restraints weight = 73956.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112944 restraints weight = 60773.057| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28985 Z= 0.172 Angle : 0.767 10.345 39108 Z= 0.391 Chirality : 0.047 0.274 4290 Planarity : 0.006 0.153 5058 Dihedral : 6.414 60.027 3867 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3526 helix: 0.74 (0.13), residues: 1556 sheet: -0.83 (0.27), residues: 366 loop : -1.85 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP C 340 HIS 0.012 0.002 HIS D 492 PHE 0.026 0.002 PHE G 669 TYR 0.031 0.002 TYR D 722 ARG 0.015 0.001 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1365) hydrogen bonds : angle 5.13502 ( 3852) covalent geometry : bond 0.00390 (28978) covalent geometry : angle 0.76746 (39108) Misc. bond : bond 0.00818 ( 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 620 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 3.099 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 47 MET cc_start: 0.6761 (tpt) cc_final: 0.6541 (tpt) REVERT: B 82 MET cc_start: 0.8264 (tpt) cc_final: 0.7907 (tpt) REVERT: B 227 MET cc_start: 0.8455 (tpt) cc_final: 0.8063 (tpp) REVERT: B 283 MET cc_start: 0.8952 (mmm) cc_final: 0.8675 (mmt) REVERT: B 325 MET cc_start: 0.7885 (mmt) cc_final: 0.7570 (mmt) REVERT: B 362 TYR cc_start: 0.8264 (t80) cc_final: 0.7927 (t80) REVERT: B 364 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7090 (mm-30) REVERT: G 95 PHE cc_start: 0.4977 (m-80) cc_final: 0.4699 (m-80) REVERT: G 98 GLU cc_start: 0.5707 (tt0) cc_final: 0.5122 (tt0) REVERT: G 277 LEU cc_start: 0.7526 (tp) cc_final: 0.6741 (tt) REVERT: G 295 PRO cc_start: 0.8433 (Cg_endo) cc_final: 0.8126 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8901 (mmpt) cc_final: 0.8617 (mmmm) REVERT: G 371 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8198 (pm20) REVERT: G 470 PHE cc_start: 0.8137 (t80) cc_final: 0.7789 (t80) REVERT: G 662 LEU cc_start: 0.8890 (tp) cc_final: 0.8565 (tp) REVERT: G 703 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7945 (ttp-170) REVERT: G 770 LEU cc_start: 0.1673 (mt) cc_final: 0.1307 (mt) REVERT: P 68 GLN cc_start: 0.8267 (mt0) cc_final: 0.7723 (mp10) REVERT: A 179 ASP cc_start: 0.8191 (t0) cc_final: 0.7605 (t0) REVERT: A 205 GLU cc_start: 0.7361 (pt0) cc_final: 0.7089 (mt-10) REVERT: A 244 ASP cc_start: 0.6807 (m-30) cc_final: 0.5971 (t0) REVERT: A 270 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6464 (mt-10) REVERT: A 299 MET cc_start: 0.7600 (mpp) cc_final: 0.7163 (mpp) REVERT: A 334 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6777 (mt-10) REVERT: A 355 MET cc_start: 0.8664 (mmp) cc_final: 0.8271 (tpp) REVERT: D 346 LYS cc_start: 0.8482 (tmtt) cc_final: 0.7999 (tttp) REVERT: D 362 MET cc_start: 0.8893 (mmp) cc_final: 0.8425 (mmt) REVERT: D 499 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 502 LYS cc_start: 0.7550 (tmtt) cc_final: 0.7201 (mmmt) REVERT: D 669 PHE cc_start: 0.5420 (m-10) cc_final: 0.5181 (m-10) REVERT: C 88 HIS cc_start: 0.8217 (t-90) cc_final: 0.7537 (t70) REVERT: C 89 THR cc_start: 0.8276 (m) cc_final: 0.7308 (m) REVERT: C 93 GLU cc_start: 0.8256 (mp0) cc_final: 0.7552 (mp0) REVERT: C 115 ASN cc_start: 0.8797 (t0) cc_final: 0.8593 (t0) REVERT: C 205 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7518 (mp0) REVERT: C 290 ARG cc_start: 0.8832 (mpt-90) cc_final: 0.8458 (mpt-90) REVERT: C 323 SER cc_start: 0.8341 (p) cc_final: 0.7966 (t) REVERT: J 43 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7018 (tmtt) REVERT: J 98 GLU cc_start: 0.6926 (tt0) cc_final: 0.6344 (pm20) REVERT: J 218 ASP cc_start: 0.7823 (m-30) cc_final: 0.6611 (p0) REVERT: J 239 ASP cc_start: 0.7809 (t0) cc_final: 0.7014 (p0) REVERT: J 357 MET cc_start: 0.8136 (mtt) cc_final: 0.7252 (mtt) REVERT: J 370 GLU cc_start: 0.6717 (pm20) cc_final: 0.5757 (tm-30) REVERT: J 433 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7985 (tm-30) REVERT: J 563 PHE cc_start: 0.7360 (t80) cc_final: 0.7116 (t80) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.3930 time to fit residues: 387.4550 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 : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 262 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 279 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 276 GLN D 486 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** 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 361 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110182 restraints weight = 75615.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109389 restraints weight = 50922.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.109761 restraints weight = 37671.907| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28985 Z= 0.174 Angle : 0.783 12.945 39108 Z= 0.398 Chirality : 0.048 0.413 4290 Planarity : 0.006 0.151 5058 Dihedral : 6.404 57.898 3867 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.22 % Favored : 91.75 % Rotamer: Outliers : 0.03 % Allowed : 0.91 % Favored : 99.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3526 helix: 0.79 (0.13), residues: 1553 sheet: -0.47 (0.28), residues: 339 loop : -1.85 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP C 340 HIS 0.018 0.002 HIS D 492 PHE 0.044 0.002 PHE D 489 TYR 0.034 0.002 TYR J 588 ARG 0.017 0.001 ARG O 125 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 1365) hydrogen bonds : angle 5.15320 ( 3852) covalent geometry : bond 0.00397 (28978) covalent geometry : angle 0.78345 (39108) Misc. bond : bond 0.00792 ( 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 606 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 605 time to evaluate : 3.125 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: 0.8192 (tpt) cc_final: 0.7830 (tpt) REVERT: B 227 MET cc_start: 0.8362 (tpt) cc_final: 0.7963 (tpp) REVERT: B 325 MET cc_start: 0.7869 (mmt) cc_final: 0.7594 (mmt) REVERT: B 334 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 340 TRP cc_start: 0.9214 (t60) cc_final: 0.8976 (t60) REVERT: B 362 TYR cc_start: 0.8320 (t80) cc_final: 0.7994 (t80) REVERT: B 364 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7208 (mm-30) REVERT: G 95 PHE cc_start: 0.4784 (m-80) cc_final: 0.4544 (m-80) REVERT: G 98 GLU cc_start: 0.5684 (tt0) cc_final: 0.5209 (tt0) REVERT: G 277 LEU cc_start: 0.7062 (tp) cc_final: 0.6753 (tt) REVERT: G 295 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7942 (Cg_exo) REVERT: G 334 ASN cc_start: 0.8657 (t0) cc_final: 0.8420 (t0) REVERT: G 363 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8702 (mmmm) REVERT: G 371 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8231 (pm20) REVERT: G 470 PHE cc_start: 0.8230 (t80) cc_final: 0.7814 (t80) REVERT: G 478 ILE cc_start: 0.8686 (mm) cc_final: 0.8442 (tp) REVERT: G 703 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.8060 (ttt-90) REVERT: G 770 LEU cc_start: 0.2051 (mt) cc_final: 0.1587 (mt) REVERT: P 68 GLN cc_start: 0.8381 (mt0) cc_final: 0.7783 (mp10) REVERT: P 132 SER cc_start: 0.8412 (m) cc_final: 0.7905 (p) REVERT: P 139 GLU cc_start: 0.7808 (pt0) cc_final: 0.7170 (tp30) REVERT: P 141 MET cc_start: 0.7916 (mmm) cc_final: 0.7687 (mmm) REVERT: A 179 ASP cc_start: 0.8267 (t0) cc_final: 0.7648 (t0) REVERT: A 205 GLU cc_start: 0.7401 (pt0) cc_final: 0.7151 (mt-10) REVERT: A 244 ASP cc_start: 0.6957 (m-30) cc_final: 0.6108 (t0) REVERT: A 270 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6447 (mt-10) REVERT: A 299 MET cc_start: 0.7601 (mpp) cc_final: 0.7161 (mpp) REVERT: A 334 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6972 (mt-10) REVERT: A 355 MET cc_start: 0.8721 (mmp) cc_final: 0.8350 (tpp) REVERT: D 346 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8028 (tttp) REVERT: D 362 MET cc_start: 0.9008 (mmp) cc_final: 0.8550 (mmt) REVERT: D 453 ARG cc_start: 0.6820 (ptm-80) cc_final: 0.6403 (ptt-90) REVERT: D 499 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 502 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7257 (mmmt) REVERT: D 522 ASP cc_start: 0.8441 (m-30) cc_final: 0.8191 (m-30) REVERT: C 88 HIS cc_start: 0.8225 (t-90) cc_final: 0.7937 (t-90) REVERT: C 132 MET cc_start: 0.8468 (tmm) cc_final: 0.7844 (tmm) REVERT: C 147 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6247 (ptm160) REVERT: C 244 ASP cc_start: 0.8288 (p0) cc_final: 0.7231 (t0) REVERT: C 290 ARG cc_start: 0.8925 (mpt-90) cc_final: 0.8648 (mpt-90) REVERT: C 296 ASN cc_start: 0.8365 (m-40) cc_final: 0.7475 (m-40) REVERT: C 305 MET cc_start: 0.7619 (mpp) cc_final: 0.7303 (mtt) REVERT: C 323 SER cc_start: 0.8391 (p) cc_final: 0.8028 (t) REVERT: J 218 ASP cc_start: 0.8063 (m-30) cc_final: 0.6792 (p0) REVERT: J 357 MET cc_start: 0.8420 (mtt) cc_final: 0.7480 (mtt) REVERT: J 380 GLU cc_start: 0.6566 (pm20) cc_final: 0.6302 (pm20) REVERT: J 433 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8196 (tm-30) REVERT: J 466 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8410 (mm-30) REVERT: J 563 PHE cc_start: 0.7550 (t80) cc_final: 0.7342 (t80) outliers start: 1 outliers final: 0 residues processed: 606 average time/residue: 0.4249 time to fit residues: 412.6824 Evaluate side-chains 459 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 266 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 170 optimal weight: 0.0060 chunk 17 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- 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 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** A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 581 HIS ** 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 314 GLN J 187 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.138830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108625 restraints weight = 75930.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107692 restraints weight = 54112.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107719 restraints weight = 43487.047| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28985 Z= 0.204 Angle : 0.804 10.487 39108 Z= 0.412 Chirality : 0.049 0.349 4290 Planarity : 0.006 0.136 5058 Dihedral : 6.424 56.283 3867 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.11 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3526 helix: 0.70 (0.13), residues: 1565 sheet: -0.49 (0.28), residues: 339 loop : -1.90 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.004 TRP C 340 HIS 0.017 0.002 HIS D 492 PHE 0.047 0.003 PHE D 489 TYR 0.049 0.002 TYR G 310 ARG 0.015 0.001 ARG P 167 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 1365) hydrogen bonds : angle 5.21696 ( 3852) covalent geometry : bond 0.00468 (28978) covalent geometry : angle 0.80436 (39108) Misc. bond : bond 0.00446 ( 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 572 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 3.147 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: 0.8279 (tpt) cc_final: 0.7883 (tpt) REVERT: B 148 THR cc_start: 0.9101 (t) cc_final: 0.8824 (m) REVERT: B 227 MET cc_start: 0.8351 (tpt) cc_final: 0.7944 (tpp) REVERT: B 325 MET cc_start: 0.8011 (mmt) cc_final: 0.7630 (mmt) REVERT: B 362 TYR cc_start: 0.8334 (t80) cc_final: 0.7909 (t80) REVERT: B 364 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7294 (mm-30) REVERT: G 98 GLU cc_start: 0.5781 (tt0) cc_final: 0.5226 (tt0) REVERT: G 277 LEU cc_start: 0.7591 (tp) cc_final: 0.6780 (tp) REVERT: G 295 PRO cc_start: 0.8293 (Cg_endo) cc_final: 0.7924 (Cg_exo) REVERT: G 334 ASN cc_start: 0.8742 (t0) cc_final: 0.8496 (t0) REVERT: G 363 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8762 (mmmm) REVERT: G 371 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8241 (pm20) REVERT: G 470 PHE cc_start: 0.8196 (t80) cc_final: 0.7829 (t80) REVERT: G 770 LEU cc_start: 0.2433 (mt) cc_final: 0.1902 (mt) REVERT: P 68 GLN cc_start: 0.8360 (mt0) cc_final: 0.7768 (mp10) REVERT: P 132 SER cc_start: 0.8425 (m) cc_final: 0.7894 (p) REVERT: P 141 MET cc_start: 0.8000 (mmm) cc_final: 0.7683 (mmm) REVERT: A 179 ASP cc_start: 0.8238 (t0) cc_final: 0.7631 (t0) REVERT: A 244 ASP cc_start: 0.6470 (m-30) cc_final: 0.5663 (t0) REVERT: A 270 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6446 (mt-10) REVERT: A 334 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6839 (mt-10) REVERT: A 355 MET cc_start: 0.8794 (mmp) cc_final: 0.8476 (tpp) REVERT: D 153 HIS cc_start: 0.6642 (t-90) cc_final: 0.6426 (t70) REVERT: D 189 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7561 (mptt) REVERT: D 244 PHE cc_start: 0.7828 (p90) cc_final: 0.7596 (p90) REVERT: D 346 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8010 (tttp) REVERT: D 362 MET cc_start: 0.9007 (mmp) cc_final: 0.8583 (mmt) REVERT: D 453 ARG cc_start: 0.6974 (ptm-80) cc_final: 0.6425 (ptt-90) REVERT: D 455 TYR cc_start: 0.5619 (m-10) cc_final: 0.5230 (m-80) REVERT: D 499 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 502 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7357 (mmtt) REVERT: D 522 ASP cc_start: 0.8576 (m-30) cc_final: 0.8309 (m-30) REVERT: D 721 ARG cc_start: 0.6181 (mtp180) cc_final: 0.4585 (mtm-85) REVERT: C 89 THR cc_start: 0.8356 (m) cc_final: 0.7237 (m) REVERT: C 93 GLU cc_start: 0.8409 (mp0) cc_final: 0.7642 (mp0) REVERT: C 132 MET cc_start: 0.8591 (tmm) cc_final: 0.7929 (tmm) REVERT: C 147 ARG cc_start: 0.7132 (ptp-110) cc_final: 0.6402 (ptm160) REVERT: C 290 ARG cc_start: 0.8943 (mpt-90) cc_final: 0.8603 (mpt-90) REVERT: C 296 ASN cc_start: 0.8432 (m-40) cc_final: 0.7439 (m-40) REVERT: C 305 MET cc_start: 0.7762 (mpp) cc_final: 0.7339 (mtt) REVERT: C 326 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8415 (mmtt) REVERT: C 352 PHE cc_start: 0.7736 (t80) cc_final: 0.7158 (t80) REVERT: J 339 LEU cc_start: 0.7571 (mt) cc_final: 0.7114 (mt) REVERT: J 357 MET cc_start: 0.8465 (mtt) cc_final: 0.7462 (mtt) REVERT: J 380 GLU cc_start: 0.6631 (pm20) cc_final: 0.6343 (pm20) REVERT: J 433 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8209 (tm-30) REVERT: J 466 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8452 (mm-30) outliers start: 0 outliers final: 0 residues processed: 572 average time/residue: 0.4424 time to fit residues: 407.6838 Evaluate side-chains 443 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 192 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 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** G 645 GLN A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN D 486 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.142032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113902 restraints weight = 76453.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113452 restraints weight = 70895.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114716 restraints weight = 51403.271| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28985 Z= 0.154 Angle : 0.774 10.709 39108 Z= 0.391 Chirality : 0.048 0.318 4290 Planarity : 0.006 0.147 5058 Dihedral : 6.232 56.367 3867 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3526 helix: 0.83 (0.13), residues: 1550 sheet: -0.40 (0.27), residues: 369 loop : -1.86 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.004 TRP C 340 HIS 0.016 0.001 HIS D 492 PHE 0.038 0.002 PHE D 489 TYR 0.040 0.002 TYR D 103 ARG 0.015 0.001 ARG P 167 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1365) hydrogen bonds : angle 5.11904 ( 3852) covalent geometry : bond 0.00345 (28978) covalent geometry : angle 0.77383 (39108) Misc. bond : bond 0.00328 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10912.29 seconds wall clock time: 194 minutes 6.50 seconds (11646.50 seconds total)