Starting phenix.real_space_refine on Wed Mar 4 17:54:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5k_26353/03_2026/7u5k_26353.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9552 2.51 5 N 2596 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15316 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 469} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Restraints were copied for chains: B, C, D Time building chain proxies: 3.03, per 1000 atoms: 0.20 Number of scatterers: 15316 At special positions: 0 Unit cell: (129.47, 95.23, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3096 8.00 N 2596 7.00 C 9552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 628.9 milliseconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 40.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.851A pdb=" N SER A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.981A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.628A pdb=" N PHE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.982A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 Processing helix chain 'B' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.629A pdb=" N PHE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.981A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.612A pdb=" N GLU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.641A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.250A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.629A pdb=" N PHE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.982A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP D 291 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 301 removed outlier: 3.628A pdb=" N PHE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 323 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 56 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 410 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 447 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP A 412 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 445 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 416 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 418 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 437 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.277A pdb=" N GLY A 69 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 105 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP A 71 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N HIS A 107 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS A 73 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 102 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER A 136 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 104 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 106 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP A 140 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 108 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA A 195 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 253 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 197 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 56 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL B 410 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 447 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP B 412 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 445 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER B 416 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 418 " --> pdb=" O CYS B 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET B 437 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU B 444 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 455 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY B 69 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 105 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 71 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N HIS B 107 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N HIS B 73 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 102 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER B 136 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 104 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS B 138 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 106 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP B 140 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 108 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA B 195 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 253 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 197 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 56 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 64 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL C 410 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 447 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP C 412 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 445 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 416 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 418 " --> pdb=" O CYS C 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET C 437 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU C 444 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 455 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY C 69 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 105 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 71 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS C 107 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS C 73 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 102 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER C 136 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 104 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS C 138 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP C 106 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP C 140 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 108 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 195 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 253 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 197 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 56 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET D 64 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL D 410 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE D 447 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP D 412 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 445 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER D 416 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 418 " --> pdb=" O CYS D 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET D 437 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU D 444 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU D 455 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY D 69 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE D 105 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP D 71 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS D 107 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS D 73 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 195 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR D 253 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 197 " --> pdb=" O THR D 253 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1884 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: 2.17 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5077 1.34 - 1.46: 2909 1.46 - 1.58: 7378 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15480 Sorted by residual: bond pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.32e+00 bond pdb=" N LYS D 43 " pdb=" CA LYS D 43 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 6.02e+00 bond pdb=" N LYS A 146 " pdb=" CA LYS A 146 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N LYS C 43 " pdb=" CA LYS C 43 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.28e-02 6.10e+03 5.78e+00 ... (remaining 15475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 20842 2.68 - 5.36: 150 5.36 - 8.04: 12 8.04 - 10.73: 4 10.73 - 13.41: 4 Bond angle restraints: 21012 Sorted by residual: angle pdb=" N PRO A 79 " pdb=" CD PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 103.20 97.72 5.48 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO C 79 " pdb=" CD PRO C 79 " pdb=" CG PRO C 79 " ideal model delta sigma weight residual 103.20 97.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO B 79 " pdb=" CD PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 103.20 97.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO D 79 " pdb=" CD PRO D 79 " pdb=" CG PRO D 79 " ideal model delta sigma weight residual 103.20 97.75 5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" N LEU C 444 " pdb=" CA LEU C 444 " pdb=" C LEU C 444 " ideal model delta sigma weight residual 112.45 107.46 4.99 1.39e+00 5.18e-01 1.29e+01 ... (remaining 21007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 7836 16.21 - 32.42: 960 32.42 - 48.63: 336 48.63 - 64.84: 120 64.84 - 81.05: 28 Dihedral angle restraints: 9280 sinusoidal: 3644 harmonic: 5636 Sorted by residual: dihedral pdb=" CA LEU B 137 " pdb=" C LEU B 137 " pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU A 137 " pdb=" C LEU A 137 " pdb=" N HIS A 138 " pdb=" CA HIS A 138 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU C 137 " pdb=" C LEU C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 9277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1688 0.038 - 0.075: 442 0.075 - 0.113: 182 0.113 - 0.151: 52 0.151 - 0.189: 8 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA LEU D 444 " pdb=" N LEU D 444 " pdb=" C LEU D 444 " pdb=" CB LEU D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA LEU C 444 " pdb=" N LEU C 444 " pdb=" C LEU C 444 " pdb=" CB LEU C 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA LEU A 444 " pdb=" N LEU A 444 " pdb=" C LEU A 444 " pdb=" CB LEU A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2369 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 219 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO C 220 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 219 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 220 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 219 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 220 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 220 " -0.031 5.00e-02 4.00e+02 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 16 2.15 - 2.84: 5003 2.84 - 3.53: 22799 3.53 - 4.21: 41895 4.21 - 4.90: 70505 Nonbonded interactions: 140218 Sorted by model distance: nonbonded pdb=" OD2 ASP A 178 " pdb=" O HOH A 601 " model vdw 1.465 3.040 nonbonded pdb=" OD2 ASP C 178 " pdb=" O HOH C 601 " model vdw 1.477 3.040 nonbonded pdb=" OD2 ASP D 178 " pdb=" O HOH D 601 " model vdw 1.478 3.040 nonbonded pdb=" OD2 ASP B 178 " pdb=" O HOH B 601 " model vdw 1.483 3.040 nonbonded pdb=" NH2 ARG D 487 " pdb=" O HOH D 602 " model vdw 1.953 3.120 ... (remaining 140213 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.003 0.047 15480 Z= 0.166 Angle : 0.638 13.407 21012 Z= 0.359 Chirality : 0.044 0.189 2372 Planarity : 0.005 0.055 2740 Dihedral : 17.745 81.050 5664 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 24.94 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 1964 helix: 0.89 (0.19), residues: 756 sheet: -1.39 (0.31), residues: 236 loop : 0.04 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 173 TYR 0.008 0.001 TYR B 182 PHE 0.008 0.001 PHE A 380 TRP 0.013 0.001 TRP B 412 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00287 (15480) covalent geometry : angle 0.63788 (21012) hydrogen bonds : bond 0.11946 ( 612) hydrogen bonds : angle 6.71999 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.481 Fit side-chains REVERT: A 43 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7756 (mmtp) REVERT: A 64 MET cc_start: 0.8164 (mtp) cc_final: 0.7736 (ptp) REVERT: A 87 ASP cc_start: 0.7906 (m-30) cc_final: 0.7308 (m-30) REVERT: A 130 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6470 (ptpp) REVERT: A 262 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 266 GLN cc_start: 0.7563 (mt0) cc_final: 0.7045 (mp-120) REVERT: A 367 ASP cc_start: 0.7799 (t70) cc_final: 0.7350 (t0) REVERT: A 483 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7488 (mmtp) REVERT: B 43 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7771 (mmtp) REVERT: B 64 MET cc_start: 0.8177 (mtp) cc_final: 0.7647 (ptp) REVERT: B 87 ASP cc_start: 0.7874 (m-30) cc_final: 0.7278 (m-30) REVERT: B 122 GLN cc_start: 0.7560 (tt0) cc_final: 0.7151 (tp-100) REVERT: B 130 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6449 (ptpp) REVERT: B 153 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 217 ILE cc_start: 0.7745 (mt) cc_final: 0.7544 (tp) REVERT: B 229 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: B 266 GLN cc_start: 0.7587 (mt0) cc_final: 0.7188 (mm110) REVERT: B 367 ASP cc_start: 0.7776 (t70) cc_final: 0.7317 (t0) REVERT: B 483 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7467 (mmtp) REVERT: C 43 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7729 (mmtp) REVERT: C 64 MET cc_start: 0.8168 (mtp) cc_final: 0.7623 (ptp) REVERT: C 87 ASP cc_start: 0.7904 (m-30) cc_final: 0.7311 (m-30) REVERT: C 122 GLN cc_start: 0.7545 (tt0) cc_final: 0.7147 (tp-100) REVERT: C 130 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6489 (ptpp) REVERT: C 229 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: C 266 GLN cc_start: 0.7584 (mt0) cc_final: 0.7241 (mm110) REVERT: C 367 ASP cc_start: 0.7800 (t70) cc_final: 0.7342 (t0) REVERT: C 460 HIS cc_start: 0.7111 (m-70) cc_final: 0.6692 (m-70) REVERT: C 483 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7490 (mmtp) REVERT: D 43 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7720 (mmtp) REVERT: D 64 MET cc_start: 0.8178 (mtp) cc_final: 0.7635 (ptp) REVERT: D 87 ASP cc_start: 0.7877 (m-30) cc_final: 0.7292 (m-30) REVERT: D 130 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6498 (ptpp) REVERT: D 153 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7049 (mt-10) REVERT: D 229 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: D 266 GLN cc_start: 0.7554 (mt0) cc_final: 0.7054 (mp-120) REVERT: D 367 ASP cc_start: 0.7806 (t70) cc_final: 0.7346 (t0) REVERT: D 419 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7605 (m) outliers start: 41 outliers final: 28 residues processed: 323 average time/residue: 0.5930 time to fit residues: 210.5254 Evaluate side-chains 318 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 356 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 356 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C 356 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 356 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.148856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.126651 restraints weight = 15810.260| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.09 r_work: 0.3126 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15480 Z= 0.167 Angle : 0.589 13.385 21012 Z= 0.299 Chirality : 0.045 0.150 2372 Planarity : 0.005 0.052 2740 Dihedral : 6.864 49.411 2166 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.57 % Allowed : 21.55 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 1964 helix: 1.01 (0.19), residues: 756 sheet: -1.55 (0.33), residues: 228 loop : 0.08 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 471 TYR 0.015 0.002 TYR B 479 PHE 0.010 0.002 PHE C 89 TRP 0.006 0.001 TRP D 295 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00380 (15480) covalent geometry : angle 0.58932 (21012) hydrogen bonds : bond 0.03665 ( 612) hydrogen bonds : angle 5.01449 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 293 time to evaluate : 0.389 Fit side-chains REVERT: A 43 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8246 (mmtp) REVERT: A 83 MET cc_start: 0.6949 (mtm) cc_final: 0.6349 (mtp) REVERT: A 130 LYS cc_start: 0.7436 (pttt) cc_final: 0.7093 (ptpp) REVERT: A 229 GLU cc_start: 0.7394 (pt0) cc_final: 0.6993 (pm20) REVERT: A 262 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 315 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7723 (t70) REVERT: A 367 ASP cc_start: 0.8221 (t70) cc_final: 0.7847 (t0) REVERT: A 379 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: A 451 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7588 (mttt) REVERT: B 59 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: B 83 MET cc_start: 0.6924 (mtm) cc_final: 0.6351 (mtp) REVERT: B 130 LYS cc_start: 0.7425 (pttt) cc_final: 0.6934 (ptpp) REVERT: B 229 GLU cc_start: 0.7297 (pt0) cc_final: 0.6751 (pm20) REVERT: B 315 ASP cc_start: 0.8035 (m-30) cc_final: 0.7733 (t70) REVERT: B 367 ASP cc_start: 0.8209 (t70) cc_final: 0.7819 (t0) REVERT: B 379 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: B 451 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7720 (mtpt) REVERT: C 20 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7298 (mtpp) REVERT: C 83 MET cc_start: 0.7049 (mtm) cc_final: 0.6457 (mtp) REVERT: C 122 GLN cc_start: 0.8144 (tt0) cc_final: 0.7938 (tp-100) REVERT: C 130 LYS cc_start: 0.7453 (pttt) cc_final: 0.7097 (ptpp) REVERT: C 229 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: C 315 ASP cc_start: 0.8022 (m-30) cc_final: 0.7746 (t70) REVERT: C 367 ASP cc_start: 0.8230 (t70) cc_final: 0.7851 (t0) REVERT: C 379 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: C 451 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: C 458 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6437 (t) REVERT: C 460 HIS cc_start: 0.7845 (m-70) cc_final: 0.7540 (m-70) REVERT: D 59 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: D 83 MET cc_start: 0.6965 (mtm) cc_final: 0.6354 (mtp) REVERT: D 130 LYS cc_start: 0.7495 (pttt) cc_final: 0.7115 (ptpp) REVERT: D 229 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: D 315 ASP cc_start: 0.7986 (m-30) cc_final: 0.7727 (t70) REVERT: D 367 ASP cc_start: 0.8210 (t70) cc_final: 0.7828 (t0) REVERT: D 379 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: D 451 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7726 (mtpt) outliers start: 92 outliers final: 47 residues processed: 337 average time/residue: 0.6142 time to fit residues: 226.3922 Evaluate side-chains 336 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 294 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 294 ASN B 460 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 294 ASN D 460 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.144696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.121350 restraints weight = 16017.590| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.16 r_work: 0.3054 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15480 Z= 0.308 Angle : 0.701 13.864 21012 Z= 0.368 Chirality : 0.049 0.152 2372 Planarity : 0.006 0.052 2740 Dihedral : 6.307 40.415 2126 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.84 % Allowed : 20.22 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 1964 helix: 0.52 (0.18), residues: 748 sheet: -1.15 (0.33), residues: 228 loop : -0.15 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 227 TYR 0.020 0.003 TYR A 479 PHE 0.022 0.003 PHE C 89 TRP 0.010 0.002 TRP C 295 HIS 0.004 0.002 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00705 (15480) covalent geometry : angle 0.70136 (21012) hydrogen bonds : bond 0.04688 ( 612) hydrogen bonds : angle 5.31982 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 288 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8279 (mmtp) REVERT: A 83 MET cc_start: 0.7181 (mtm) cc_final: 0.6512 (mtp) REVERT: A 130 LYS cc_start: 0.7554 (pttt) cc_final: 0.7054 (ptpp) REVERT: A 207 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: A 229 GLU cc_start: 0.7559 (pt0) cc_final: 0.7171 (pm20) REVERT: A 262 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 266 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7549 (mm110) REVERT: A 367 ASP cc_start: 0.8335 (t70) cc_final: 0.7990 (t0) REVERT: A 440 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7549 (ttp-170) REVERT: A 451 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: B 59 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: B 83 MET cc_start: 0.7075 (mtm) cc_final: 0.6577 (mtp) REVERT: B 130 LYS cc_start: 0.7548 (pttt) cc_final: 0.7018 (ptpp) REVERT: B 207 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: B 229 GLU cc_start: 0.7461 (pt0) cc_final: 0.6754 (pm20) REVERT: B 367 ASP cc_start: 0.8328 (t70) cc_final: 0.7980 (t0) REVERT: B 451 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8010 (mtpt) REVERT: C 20 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7356 (mtpp) REVERT: C 83 MET cc_start: 0.7252 (mtm) cc_final: 0.6641 (mtp) REVERT: C 122 GLN cc_start: 0.8118 (tt0) cc_final: 0.7867 (tp-100) REVERT: C 207 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: C 229 GLU cc_start: 0.7611 (pt0) cc_final: 0.6879 (pm20) REVERT: C 266 GLN cc_start: 0.8121 (mm110) cc_final: 0.7851 (mm110) REVERT: C 367 ASP cc_start: 0.8329 (t70) cc_final: 0.7988 (t0) REVERT: C 451 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8019 (mtpt) REVERT: C 460 HIS cc_start: 0.7956 (m-70) cc_final: 0.7619 (m-70) REVERT: D 59 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: D 83 MET cc_start: 0.7160 (mtm) cc_final: 0.6579 (mtp) REVERT: D 130 LYS cc_start: 0.7598 (pttt) cc_final: 0.7097 (ptpp) REVERT: D 207 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: D 229 GLU cc_start: 0.7593 (pt0) cc_final: 0.6832 (pm20) REVERT: D 266 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7550 (mm110) REVERT: D 451 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (mtpt) outliers start: 113 outliers final: 63 residues processed: 342 average time/residue: 0.6598 time to fit residues: 245.9457 Evaluate side-chains 356 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 14 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS D 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.149569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.127639 restraints weight = 15855.357| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.09 r_work: 0.3130 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15480 Z= 0.126 Angle : 0.551 12.709 21012 Z= 0.279 Chirality : 0.043 0.129 2372 Planarity : 0.004 0.050 2740 Dihedral : 5.600 40.667 2120 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.84 % Allowed : 22.40 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 1964 helix: 0.83 (0.19), residues: 756 sheet: -1.44 (0.34), residues: 228 loop : -0.01 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 471 TYR 0.012 0.002 TYR B 479 PHE 0.007 0.001 PHE D 89 TRP 0.011 0.001 TRP D 295 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00287 (15480) covalent geometry : angle 0.55145 (21012) hydrogen bonds : bond 0.03327 ( 612) hydrogen bonds : angle 4.67872 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8231 (mmtp) REVERT: A 83 MET cc_start: 0.7111 (mtm) cc_final: 0.6534 (mtp) REVERT: A 130 LYS cc_start: 0.7429 (pttt) cc_final: 0.7011 (ptpp) REVERT: A 229 GLU cc_start: 0.7454 (pt0) cc_final: 0.7152 (pm20) REVERT: A 266 GLN cc_start: 0.7953 (mp10) cc_final: 0.7408 (tm-30) REVERT: A 367 ASP cc_start: 0.8254 (t70) cc_final: 0.7864 (t0) REVERT: A 435 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: B 59 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 83 MET cc_start: 0.7002 (mtm) cc_final: 0.6516 (mtp) REVERT: B 130 LYS cc_start: 0.7491 (pttt) cc_final: 0.6959 (ptpp) REVERT: B 207 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: B 229 GLU cc_start: 0.7428 (pt0) cc_final: 0.6772 (pm20) REVERT: B 367 ASP cc_start: 0.8250 (t70) cc_final: 0.7873 (t0) REVERT: B 435 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 451 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7839 (mtpt) REVERT: B 505 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.5053 (tm-30) REVERT: C 20 LYS cc_start: 0.7578 (mtmt) cc_final: 0.7297 (mtpp) REVERT: C 83 MET cc_start: 0.7159 (mtm) cc_final: 0.6624 (mtp) REVERT: C 122 GLN cc_start: 0.8127 (tt0) cc_final: 0.7912 (tp-100) REVERT: C 130 LYS cc_start: 0.7715 (mttp) cc_final: 0.7389 (mttt) REVERT: C 207 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: C 229 GLU cc_start: 0.7409 (pt0) cc_final: 0.6807 (pm20) REVERT: C 266 GLN cc_start: 0.8032 (mm110) cc_final: 0.7798 (mm110) REVERT: C 367 ASP cc_start: 0.8267 (t70) cc_final: 0.7893 (t0) REVERT: C 451 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (mtpt) REVERT: C 460 HIS cc_start: 0.7861 (m90) cc_final: 0.7605 (m-70) REVERT: C 505 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4994 (tm-30) REVERT: D 20 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7380 (mtmt) REVERT: D 59 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: D 83 MET cc_start: 0.7138 (mtm) cc_final: 0.6581 (mtp) REVERT: D 130 LYS cc_start: 0.7508 (pttt) cc_final: 0.7051 (ptpp) REVERT: D 207 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: D 229 GLU cc_start: 0.7438 (pt0) cc_final: 0.6763 (pm20) REVERT: D 266 GLN cc_start: 0.7905 (mp10) cc_final: 0.7463 (mm110) REVERT: D 367 ASP cc_start: 0.8255 (t70) cc_final: 0.7880 (t0) REVERT: D 451 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7843 (mtpt) REVERT: D 460 HIS cc_start: 0.7819 (m90) cc_final: 0.7386 (m-70) REVERT: D 483 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8141 (mmtp) REVERT: D 505 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.5067 (tm-30) outliers start: 80 outliers final: 48 residues processed: 335 average time/residue: 0.6609 time to fit residues: 242.0171 Evaluate side-chains 337 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 449 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 426 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.122831 restraints weight = 15949.332| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.12 r_work: 0.3077 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15480 Z= 0.248 Angle : 0.640 13.382 21012 Z= 0.331 Chirality : 0.047 0.145 2372 Planarity : 0.005 0.049 2740 Dihedral : 5.805 39.165 2117 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.93 % Allowed : 21.43 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 1964 helix: 0.59 (0.18), residues: 752 sheet: -1.00 (0.34), residues: 228 loop : -0.14 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 173 TYR 0.020 0.003 TYR C 479 PHE 0.016 0.002 PHE D 89 TRP 0.010 0.002 TRP D 295 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00569 (15480) covalent geometry : angle 0.64005 (21012) hydrogen bonds : bond 0.04135 ( 612) hydrogen bonds : angle 5.01717 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 277 time to evaluate : 0.473 Fit side-chains REVERT: A 43 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8287 (mmtp) REVERT: A 83 MET cc_start: 0.7201 (mtm) cc_final: 0.6620 (mtp) REVERT: A 130 LYS cc_start: 0.7578 (pttt) cc_final: 0.7066 (ptpp) REVERT: A 229 GLU cc_start: 0.7532 (pt0) cc_final: 0.7195 (pm20) REVERT: A 262 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 367 ASP cc_start: 0.8315 (t70) cc_final: 0.7961 (t0) REVERT: A 435 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: A 505 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4978 (tm-30) REVERT: B 59 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 83 MET cc_start: 0.7095 (mtm) cc_final: 0.6688 (mtp) REVERT: B 130 LYS cc_start: 0.7572 (pttt) cc_final: 0.7048 (ptpp) REVERT: B 207 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: B 229 GLU cc_start: 0.7446 (pt0) cc_final: 0.6781 (pm20) REVERT: B 367 ASP cc_start: 0.8312 (t70) cc_final: 0.7949 (t0) REVERT: B 451 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8013 (mtpt) REVERT: B 459 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7781 (mt) REVERT: C 20 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7336 (mtpp) REVERT: C 83 MET cc_start: 0.7239 (mtm) cc_final: 0.6721 (mtp) REVERT: C 122 GLN cc_start: 0.8133 (tt0) cc_final: 0.7920 (tp-100) REVERT: C 207 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: C 229 GLU cc_start: 0.7569 (pt0) cc_final: 0.6919 (pm20) REVERT: C 266 GLN cc_start: 0.8105 (mm110) cc_final: 0.7840 (mm110) REVERT: C 367 ASP cc_start: 0.8318 (t70) cc_final: 0.7962 (t0) REVERT: C 451 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (mtpt) REVERT: C 460 HIS cc_start: 0.7953 (m90) cc_final: 0.7597 (m-70) REVERT: D 59 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: D 83 MET cc_start: 0.7169 (mtm) cc_final: 0.6672 (mtp) REVERT: D 207 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: D 229 GLU cc_start: 0.7588 (pt0) cc_final: 0.6883 (pm20) REVERT: D 367 ASP cc_start: 0.8316 (t70) cc_final: 0.7964 (t0) REVERT: D 451 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8023 (mtpt) REVERT: D 459 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7706 (mt) REVERT: D 460 HIS cc_start: 0.7952 (m90) cc_final: 0.7683 (m90) outliers start: 98 outliers final: 66 residues processed: 329 average time/residue: 0.6356 time to fit residues: 229.0223 Evaluate side-chains 347 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 269 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 122 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.148919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.127097 restraints weight = 15796.498| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.08 r_work: 0.3132 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15480 Z= 0.138 Angle : 0.562 12.928 21012 Z= 0.283 Chirality : 0.044 0.130 2372 Planarity : 0.004 0.049 2740 Dihedral : 5.117 26.958 2108 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.02 % Allowed : 22.58 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 1964 helix: 0.90 (0.19), residues: 756 sheet: -0.86 (0.35), residues: 228 loop : -0.11 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.012 0.002 TYR C 479 PHE 0.007 0.001 PHE A 89 TRP 0.009 0.001 TRP A 295 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00316 (15480) covalent geometry : angle 0.56249 (21012) hydrogen bonds : bond 0.03280 ( 612) hydrogen bonds : angle 4.62183 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 289 time to evaluate : 0.694 Fit side-chains REVERT: A 20 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7449 (mtmt) REVERT: A 43 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8210 (mmtp) REVERT: A 83 MET cc_start: 0.7157 (mtm) cc_final: 0.6632 (mtp) REVERT: A 130 LYS cc_start: 0.7420 (pttt) cc_final: 0.6927 (ptpp) REVERT: A 207 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: A 229 GLU cc_start: 0.7428 (pt0) cc_final: 0.7174 (pm20) REVERT: A 262 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 367 ASP cc_start: 0.8256 (t70) cc_final: 0.7873 (t0) REVERT: A 505 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.4968 (tm-30) REVERT: B 59 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 83 MET cc_start: 0.7078 (mtm) cc_final: 0.6683 (mtp) REVERT: B 130 LYS cc_start: 0.7449 (pttt) cc_final: 0.6977 (ptpp) REVERT: B 229 GLU cc_start: 0.7409 (pt0) cc_final: 0.6786 (pm20) REVERT: B 367 ASP cc_start: 0.8212 (t70) cc_final: 0.7831 (t0) REVERT: B 451 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7829 (mtpt) REVERT: C 20 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7310 (mtpp) REVERT: C 83 MET cc_start: 0.7226 (mtm) cc_final: 0.6716 (mtp) REVERT: C 130 LYS cc_start: 0.7788 (mttp) cc_final: 0.7396 (mttt) REVERT: C 207 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: C 229 GLU cc_start: 0.7434 (pt0) cc_final: 0.6830 (pm20) REVERT: C 266 GLN cc_start: 0.8038 (mm110) cc_final: 0.7808 (mm110) REVERT: C 367 ASP cc_start: 0.8236 (t70) cc_final: 0.7861 (t0) REVERT: C 451 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7818 (mtpt) REVERT: C 460 HIS cc_start: 0.7910 (m90) cc_final: 0.7584 (m-70) REVERT: D 20 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7365 (mtmt) REVERT: D 56 LYS cc_start: 0.7581 (tptp) cc_final: 0.7372 (tptm) REVERT: D 59 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: D 83 MET cc_start: 0.7116 (mtm) cc_final: 0.6652 (mtp) REVERT: D 130 LYS cc_start: 0.7697 (mttp) cc_final: 0.7445 (pttt) REVERT: D 229 GLU cc_start: 0.7531 (pt0) cc_final: 0.6854 (pm20) REVERT: D 345 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6751 (tptm) REVERT: D 367 ASP cc_start: 0.8259 (t70) cc_final: 0.7889 (t0) REVERT: D 451 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: D 459 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7712 (mt) outliers start: 83 outliers final: 52 residues processed: 326 average time/residue: 0.6244 time to fit residues: 223.1230 Evaluate side-chains 335 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 143 optimal weight: 0.0270 chunk 133 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 116 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 122 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 209 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.151106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.129560 restraints weight = 15741.326| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.15 r_work: 0.3152 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15480 Z= 0.111 Angle : 0.539 12.600 21012 Z= 0.269 Chirality : 0.043 0.131 2372 Planarity : 0.004 0.048 2740 Dihedral : 4.898 26.889 2108 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.06 % Allowed : 23.31 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1964 helix: 1.05 (0.19), residues: 760 sheet: -1.23 (0.35), residues: 228 loop : 0.06 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.009 0.002 TYR C 479 PHE 0.007 0.001 PHE C 90 TRP 0.008 0.001 TRP A 295 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00257 (15480) covalent geometry : angle 0.53907 (21012) hydrogen bonds : bond 0.02994 ( 612) hydrogen bonds : angle 4.43053 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.558 Fit side-chains REVERT: A 43 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8128 (mmtp) REVERT: A 83 MET cc_start: 0.7173 (mtm) cc_final: 0.6654 (mtp) REVERT: A 130 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6829 (ptpp) REVERT: A 229 GLU cc_start: 0.7415 (pt0) cc_final: 0.7173 (pm20) REVERT: A 262 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 367 ASP cc_start: 0.8221 (t70) cc_final: 0.7841 (t0) REVERT: A 431 TYR cc_start: 0.7803 (m-80) cc_final: 0.7579 (m-80) REVERT: A 460 HIS cc_start: 0.7910 (m-70) cc_final: 0.7457 (m-70) REVERT: B 59 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: B 64 MET cc_start: 0.8807 (mtp) cc_final: 0.8301 (ptp) REVERT: B 83 MET cc_start: 0.7045 (mtm) cc_final: 0.6694 (mtp) REVERT: B 229 GLU cc_start: 0.7347 (pt0) cc_final: 0.6784 (pm20) REVERT: B 367 ASP cc_start: 0.8195 (t70) cc_final: 0.7811 (t0) REVERT: B 431 TYR cc_start: 0.7784 (m-80) cc_final: 0.7521 (m-80) REVERT: B 451 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7832 (mtpt) REVERT: C 20 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7225 (mtpp) REVERT: C 83 MET cc_start: 0.7203 (mtm) cc_final: 0.6756 (mtp) REVERT: C 130 LYS cc_start: 0.7696 (mttp) cc_final: 0.7323 (mttt) REVERT: C 229 GLU cc_start: 0.7365 (pt0) cc_final: 0.6767 (pm20) REVERT: C 367 ASP cc_start: 0.8213 (t70) cc_final: 0.7834 (t0) REVERT: C 431 TYR cc_start: 0.7863 (m-80) cc_final: 0.7659 (m-80) REVERT: C 451 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7808 (mtpt) REVERT: C 460 HIS cc_start: 0.7868 (m90) cc_final: 0.7581 (m-70) REVERT: D 20 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7377 (mtmt) REVERT: D 59 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: D 64 MET cc_start: 0.8820 (mtp) cc_final: 0.8304 (ptp) REVERT: D 83 MET cc_start: 0.7188 (mtm) cc_final: 0.6740 (mtp) REVERT: D 130 LYS cc_start: 0.7648 (mttp) cc_final: 0.7441 (pttt) REVERT: D 229 GLU cc_start: 0.7378 (pt0) cc_final: 0.6722 (pm20) REVERT: D 367 ASP cc_start: 0.8222 (t70) cc_final: 0.7844 (t0) REVERT: D 431 TYR cc_start: 0.7803 (m-80) cc_final: 0.7537 (m-80) REVERT: D 451 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7809 (mtpt) REVERT: D 460 HIS cc_start: 0.7772 (m90) cc_final: 0.7562 (m90) outliers start: 67 outliers final: 48 residues processed: 313 average time/residue: 0.6309 time to fit residues: 216.2199 Evaluate side-chains 328 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 0.0010 chunk 158 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 266 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 77 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 = 0.3551 r_free = 0.3551 target = 0.153006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.133146 restraints weight = 15824.486| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.99 r_work: 0.3183 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15480 Z= 0.113 Angle : 0.544 12.564 21012 Z= 0.271 Chirality : 0.043 0.128 2372 Planarity : 0.004 0.047 2740 Dihedral : 4.850 27.046 2108 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.06 % Allowed : 23.85 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1964 helix: 1.11 (0.19), residues: 760 sheet: -1.06 (0.36), residues: 228 loop : 0.12 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 173 TYR 0.010 0.002 TYR C 479 PHE 0.007 0.001 PHE C 90 TRP 0.008 0.001 TRP A 295 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00263 (15480) covalent geometry : angle 0.54436 (21012) hydrogen bonds : bond 0.02958 ( 612) hydrogen bonds : angle 4.38396 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 0.526 Fit side-chains REVERT: A 64 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8334 (ptp) REVERT: A 83 MET cc_start: 0.7154 (mtm) cc_final: 0.6681 (mtp) REVERT: A 130 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6814 (ptpp) REVERT: A 229 GLU cc_start: 0.7358 (pt0) cc_final: 0.7156 (pm20) REVERT: A 262 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 367 ASP cc_start: 0.8186 (t70) cc_final: 0.7804 (t0) REVERT: A 460 HIS cc_start: 0.7833 (m-70) cc_final: 0.7386 (m-70) REVERT: A 505 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.4927 (tm-30) REVERT: B 58 ILE cc_start: 0.8308 (mp) cc_final: 0.8087 (pt) REVERT: B 59 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: B 64 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8270 (ptp) REVERT: B 83 MET cc_start: 0.7026 (mtm) cc_final: 0.6685 (mtp) REVERT: B 229 GLU cc_start: 0.7257 (pt0) cc_final: 0.6725 (pm20) REVERT: B 362 MET cc_start: 0.8602 (mtm) cc_final: 0.8275 (mtm) REVERT: B 367 ASP cc_start: 0.8164 (t70) cc_final: 0.7778 (t0) REVERT: B 431 TYR cc_start: 0.7847 (m-80) cc_final: 0.7545 (m-80) REVERT: B 451 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (mtpt) REVERT: C 20 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7193 (mtpp) REVERT: C 64 MET cc_start: 0.8774 (mtp) cc_final: 0.8269 (ptp) REVERT: C 83 MET cc_start: 0.7200 (mtm) cc_final: 0.6795 (mtp) REVERT: C 229 GLU cc_start: 0.7314 (pt0) cc_final: 0.6767 (pm20) REVERT: C 367 ASP cc_start: 0.8167 (t70) cc_final: 0.7782 (t0) REVERT: C 431 TYR cc_start: 0.7862 (m-80) cc_final: 0.7619 (m-80) REVERT: C 451 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: C 460 HIS cc_start: 0.7851 (m90) cc_final: 0.7572 (m-70) REVERT: D 16 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7275 (mtp-110) REVERT: D 20 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7327 (mtmt) REVERT: D 59 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: D 64 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8305 (ptp) REVERT: D 83 MET cc_start: 0.7172 (mtm) cc_final: 0.6756 (mtp) REVERT: D 229 GLU cc_start: 0.7275 (pt0) cc_final: 0.6686 (pm20) REVERT: D 367 ASP cc_start: 0.8184 (t70) cc_final: 0.7815 (t0) REVERT: D 451 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7809 (mtpt) outliers start: 67 outliers final: 46 residues processed: 322 average time/residue: 0.6302 time to fit residues: 222.6833 Evaluate side-chains 331 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 194 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 209 GLN B 460 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 426 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.147571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.124447 restraints weight = 15683.505| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.15 r_work: 0.3099 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15480 Z= 0.203 Angle : 0.627 13.370 21012 Z= 0.320 Chirality : 0.046 0.145 2372 Planarity : 0.005 0.046 2740 Dihedral : 5.321 27.998 2108 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.36 % Allowed : 23.91 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1964 helix: 0.85 (0.18), residues: 756 sheet: -1.07 (0.36), residues: 228 loop : 0.04 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 173 TYR 0.017 0.003 TYR B 479 PHE 0.013 0.002 PHE D 89 TRP 0.008 0.001 TRP D 295 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00472 (15480) covalent geometry : angle 0.62665 (21012) hydrogen bonds : bond 0.03729 ( 612) hydrogen bonds : angle 4.73382 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.599 Fit side-chains REVERT: A 83 MET cc_start: 0.7213 (mtm) cc_final: 0.6718 (mtp) REVERT: A 229 GLU cc_start: 0.7448 (pt0) cc_final: 0.7147 (pm20) REVERT: A 262 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 367 ASP cc_start: 0.8310 (t70) cc_final: 0.7943 (t0) REVERT: A 376 ASP cc_start: 0.8466 (p0) cc_final: 0.8237 (p0) REVERT: A 460 HIS cc_start: 0.7904 (m-70) cc_final: 0.7399 (m-70) REVERT: A 505 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.4938 (tm-30) REVERT: B 59 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: B 83 MET cc_start: 0.7113 (mtm) cc_final: 0.6773 (mtp) REVERT: B 229 GLU cc_start: 0.7326 (pt0) cc_final: 0.6737 (pm20) REVERT: B 362 MET cc_start: 0.8683 (mtm) cc_final: 0.8293 (mtm) REVERT: B 367 ASP cc_start: 0.8298 (t70) cc_final: 0.7924 (t0) REVERT: B 376 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (p0) REVERT: B 431 TYR cc_start: 0.7947 (m-80) cc_final: 0.7674 (m-80) REVERT: B 451 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7942 (mtpt) REVERT: C 20 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7250 (mtpp) REVERT: C 83 MET cc_start: 0.7249 (mtm) cc_final: 0.6807 (mtp) REVERT: C 229 GLU cc_start: 0.7499 (pt0) cc_final: 0.6935 (pm20) REVERT: C 362 MET cc_start: 0.8665 (mtm) cc_final: 0.8247 (mtm) REVERT: C 367 ASP cc_start: 0.8319 (t70) cc_final: 0.7949 (t0) REVERT: C 376 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8140 (p0) REVERT: C 379 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: C 431 TYR cc_start: 0.7952 (m-80) cc_final: 0.7656 (m-80) REVERT: C 451 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7983 (mtpt) REVERT: C 460 HIS cc_start: 0.7893 (m90) cc_final: 0.7566 (m-70) REVERT: D 20 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7385 (mtmt) REVERT: D 59 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 83 MET cc_start: 0.7187 (mtm) cc_final: 0.6778 (mtp) REVERT: D 229 GLU cc_start: 0.7545 (pt0) cc_final: 0.6837 (pm20) REVERT: D 362 MET cc_start: 0.8662 (mtm) cc_final: 0.8270 (mtm) REVERT: D 367 ASP cc_start: 0.8319 (t70) cc_final: 0.7945 (t0) REVERT: D 376 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8177 (p0) REVERT: D 379 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: D 451 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7983 (mtpt) REVERT: D 460 HIS cc_start: 0.7857 (m-70) cc_final: 0.7656 (m90) outliers start: 72 outliers final: 52 residues processed: 297 average time/residue: 0.6482 time to fit residues: 210.6291 Evaluate side-chains 328 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 0.9990 chunk 96 optimal weight: 0.0050 chunk 174 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 460 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 77 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 = 0.3501 r_free = 0.3501 target = 0.148722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.126523 restraints weight = 15775.838| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.11 r_work: 0.3123 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15480 Z= 0.167 Angle : 0.604 12.995 21012 Z= 0.305 Chirality : 0.045 0.141 2372 Planarity : 0.004 0.046 2740 Dihedral : 5.213 27.494 2108 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.75 % Allowed : 24.70 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1964 helix: 0.89 (0.18), residues: 756 sheet: -0.96 (0.37), residues: 228 loop : 0.01 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 173 TYR 0.014 0.002 TYR A 479 PHE 0.011 0.002 PHE D 89 TRP 0.008 0.001 TRP D 295 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00390 (15480) covalent geometry : angle 0.60360 (21012) hydrogen bonds : bond 0.03435 ( 612) hydrogen bonds : angle 4.64567 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.573 Fit side-chains REVERT: A 20 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7201 (ttpp) REVERT: A 83 MET cc_start: 0.7210 (mtm) cc_final: 0.6726 (mtp) REVERT: A 207 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: A 229 GLU cc_start: 0.7418 (pt0) cc_final: 0.7164 (pm20) REVERT: A 262 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 367 ASP cc_start: 0.8266 (t70) cc_final: 0.7893 (t0) REVERT: A 376 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8217 (p0) REVERT: A 431 TYR cc_start: 0.7877 (m-80) cc_final: 0.7677 (m-80) REVERT: A 460 HIS cc_start: 0.7914 (m-70) cc_final: 0.7435 (m-70) REVERT: A 505 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4910 (tm-30) REVERT: B 59 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 83 MET cc_start: 0.7111 (mtm) cc_final: 0.6763 (mtp) REVERT: B 229 GLU cc_start: 0.7358 (pt0) cc_final: 0.6764 (pm20) REVERT: B 362 MET cc_start: 0.8658 (mtm) cc_final: 0.8250 (mtm) REVERT: B 367 ASP cc_start: 0.8251 (t70) cc_final: 0.7876 (t0) REVERT: B 376 ASP cc_start: 0.8422 (p0) cc_final: 0.7939 (p0) REVERT: B 379 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: B 431 TYR cc_start: 0.7948 (m-80) cc_final: 0.7689 (m-80) REVERT: B 451 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7952 (mtpt) REVERT: C 20 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7250 (mtpp) REVERT: C 83 MET cc_start: 0.7258 (mtm) cc_final: 0.6847 (mtp) REVERT: C 229 GLU cc_start: 0.7410 (pt0) cc_final: 0.6890 (pm20) REVERT: C 362 MET cc_start: 0.8626 (mtm) cc_final: 0.8199 (mtm) REVERT: C 367 ASP cc_start: 0.8263 (t70) cc_final: 0.7873 (t0) REVERT: C 376 ASP cc_start: 0.8421 (p0) cc_final: 0.8207 (p0) REVERT: C 431 TYR cc_start: 0.7915 (m-80) cc_final: 0.7631 (m-80) REVERT: C 451 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: C 460 HIS cc_start: 0.7859 (m90) cc_final: 0.7499 (m90) REVERT: D 59 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: D 83 MET cc_start: 0.7166 (mtm) cc_final: 0.6770 (mtp) REVERT: D 229 GLU cc_start: 0.7496 (pt0) cc_final: 0.6827 (pm20) REVERT: D 362 MET cc_start: 0.8632 (mtm) cc_final: 0.8232 (mtm) REVERT: D 367 ASP cc_start: 0.8299 (t70) cc_final: 0.7930 (t0) REVERT: D 451 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (mtpt) outliers start: 62 outliers final: 51 residues processed: 289 average time/residue: 0.6165 time to fit residues: 195.8900 Evaluate side-chains 324 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.150376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.129193 restraints weight = 15680.829| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.21 r_work: 0.3123 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15480 Z= 0.132 Angle : 0.581 12.634 21012 Z= 0.291 Chirality : 0.044 0.140 2372 Planarity : 0.004 0.046 2740 Dihedral : 5.009 27.037 2108 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.69 % Allowed : 25.06 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1964 helix: 1.03 (0.19), residues: 756 sheet: -0.79 (0.38), residues: 228 loop : 0.04 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 173 TYR 0.011 0.002 TYR D 479 PHE 0.007 0.001 PHE C 89 TRP 0.009 0.001 TRP D 295 HIS 0.006 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00312 (15480) covalent geometry : angle 0.58072 (21012) hydrogen bonds : bond 0.03135 ( 612) hydrogen bonds : angle 4.51871 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5384.24 seconds wall clock time: 92 minutes 41.16 seconds (5561.16 seconds total)