Starting phenix.real_space_refine on Fri Jul 3 20:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sni_25227/07_2026/7sni_25227.map" } resolution = 2.5 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= 0.010 sd= 0.218 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 80 5.16 5 C 10312 2.51 5 N 2816 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16533 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "C" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "D" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Time building chain proxies: 3.33, per 1000 atoms: 0.20 Number of scatterers: 16533 At special positions: 0 Unit cell: (131.97, 102.09, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 28 15.00 O 3297 8.00 N 2816 7.00 C 10312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 698.5 milliseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 43.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.474A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix removed outlier: 4.097A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.552A pdb=" N ARG A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.858A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.580A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.401A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 4.232A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.504A pdb=" N ALA A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.622A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.061A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.469A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 4.085A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.855A pdb=" N TYR B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.617A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 217 removed outlier: 4.406A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.232A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ILE B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.504A pdb=" N ALA B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.616A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.097A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.468A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 4.080A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.538A pdb=" N ARG C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.865A pdb=" N TYR C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.625A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.405A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.245A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.081A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.569A pdb=" N ALA C 318 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 320 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.614A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.100A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.468A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 4.098A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.555A pdb=" N ARG D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.861A pdb=" N TYR D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.623A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 4.409A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 4.226A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.087A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.621A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.101A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 3.614A pdb=" N ALA A 71 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 423 removed outlier: 6.525A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 231 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG A 357 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 235 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY A 359 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 237 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 3.614A pdb=" N ALA B 71 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 423 removed outlier: 6.479A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 3.620A pdb=" N ALA C 71 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 423 removed outlier: 6.479A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE C 480 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 305 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR C 482 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN C 307 " --> pdb=" O TYR C 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 3.610A pdb=" N ALA D 71 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 423 removed outlier: 6.478A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA D 231 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE D 355 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL D 233 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG D 357 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU D 235 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLY D 359 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE D 237 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE D 480 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D 305 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR D 482 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN D 307 " --> pdb=" O TYR D 482 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1923 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: 3.33 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3372 1.33 - 1.45: 3988 1.45 - 1.57: 9180 1.57 - 1.69: 44 1.69 - 1.81: 132 Bond restraints: 16716 Sorted by residual: bond pdb=" O2B NAP B 602 " pdb=" P2B NAP B 602 " ideal model delta sigma weight residual 1.736 1.588 0.148 2.00e-02 2.50e+03 5.44e+01 bond pdb=" O2B NAP C 602 " pdb=" P2B NAP C 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O2B NAP D 602 " pdb=" P2B NAP D 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O2B NAP A 602 " pdb=" P2B NAP A 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.602 0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 16711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 21928 1.80 - 3.60: 550 3.60 - 5.40: 167 5.40 - 7.20: 36 7.20 - 8.99: 15 Bond angle restraints: 22696 Sorted by residual: angle pdb=" N ASP D 313 " pdb=" CA ASP D 313 " pdb=" C ASP D 313 " ideal model delta sigma weight residual 113.21 105.47 7.74 1.15e+00 7.56e-01 4.53e+01 angle pdb=" N GLY D 314 " pdb=" CA GLY D 314 " pdb=" C GLY D 314 " ideal model delta sigma weight residual 112.54 120.06 -7.52 1.28e+00 6.10e-01 3.45e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 112.92 106.49 6.43 1.23e+00 6.61e-01 2.73e+01 angle pdb=" N ASP A 313 " pdb=" CA ASP A 313 " pdb=" C ASP A 313 " ideal model delta sigma weight residual 112.92 106.63 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N ASP C 313 " pdb=" CA ASP C 313 " pdb=" C ASP C 313 " ideal model delta sigma weight residual 112.92 106.67 6.25 1.23e+00 6.61e-01 2.58e+01 ... (remaining 22691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8818 16.75 - 33.51: 873 33.51 - 50.26: 228 50.26 - 67.02: 67 67.02 - 83.77: 46 Dihedral angle restraints: 10032 sinusoidal: 4344 harmonic: 5688 Sorted by residual: dihedral pdb=" CA ILE A 199 " pdb=" C ILE A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ILE D 199 " pdb=" C ILE D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 10029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1756 0.044 - 0.089: 467 0.089 - 0.133: 164 0.133 - 0.178: 13 0.178 - 0.222: 16 Chirality restraints: 2416 Sorted by residual: chirality pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " pdb=" N9A NAP C 602 " pdb=" O4B NAP C 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1B NAP B 602 " pdb=" C2B NAP B 602 " pdb=" N9A NAP B 602 " pdb=" O4B NAP B 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " pdb=" N9A NAP A 602 " pdb=" O4B NAP A 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2413 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 95 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C LYS D 95 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS D 95 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 96 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 223 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 222 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO D 223 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.022 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3106 2.77 - 3.30: 16028 3.30 - 3.84: 30707 3.84 - 4.37: 37737 4.37 - 4.90: 61201 Nonbonded interactions: 148779 Sorted by model distance: nonbonded pdb=" O TRP D 462 " pdb=" OG1 THR D 466 " model vdw 2.239 3.040 nonbonded pdb=" O TRP C 462 " pdb=" OG1 THR C 466 " model vdw 2.239 3.040 nonbonded pdb=" O TRP B 462 " pdb=" OG1 THR B 466 " model vdw 2.241 3.040 nonbonded pdb=" O TRP A 462 " pdb=" OG1 THR A 466 " model vdw 2.243 3.040 nonbonded pdb=" O GLY C 316 " pdb=" OG1 THR C 319 " model vdw 2.243 3.040 ... (remaining 148774 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: 0.570 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 16716 Z= 0.321 Angle : 0.767 8.995 22696 Z= 0.353 Chirality : 0.047 0.222 2416 Planarity : 0.004 0.039 2892 Dihedral : 15.875 83.770 6376 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.02 (0.19), residues: 1944 helix: 0.55 (0.20), residues: 704 sheet: -0.81 (0.25), residues: 428 loop : 0.17 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.013 0.001 TYR D 202 PHE 0.011 0.001 PHE C 452 TRP 0.020 0.002 TRP B 225 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.32 (16716) covalent geometry : angle 0.76705 / 0.35 (22696) hydrogen bonds : bond 0.16048 / 10.39 ( 681) hydrogen bonds : angle 6.97930 / 4.96 ( 1923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.673 Fit side-chains REVERT: A 443 ASP cc_start: 0.7456 (m-30) cc_final: 0.7225 (m-30) REVERT: B 443 ASP cc_start: 0.7450 (m-30) cc_final: 0.7230 (m-30) REVERT: C 443 ASP cc_start: 0.7456 (m-30) cc_final: 0.7231 (m-30) REVERT: D 443 ASP cc_start: 0.7438 (m-30) cc_final: 0.7228 (m-30) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.6302 time to fit residues: 184.5220 Evaluate side-chains 202 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.0870 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN A 186 HIS A 374 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 105 ASN B 186 HIS B 374 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS D 374 HIS ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145387 restraints weight = 18798.668| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.54 r_work: 0.3587 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16716 Z= 0.241 Angle : 0.656 6.018 22696 Z= 0.345 Chirality : 0.048 0.158 2416 Planarity : 0.005 0.048 2892 Dihedral : 11.898 87.686 2432 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 8.70 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 1944 helix: 0.45 (0.20), residues: 712 sheet: -0.95 (0.25), residues: 376 loop : 0.10 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.023 0.002 TYR B 484 PHE 0.017 0.002 PHE A 452 TRP 0.011 0.002 TRP D 225 HIS 0.005 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (16716) covalent geometry : angle 0.65594 / 0.35 (22696) hydrogen bonds : bond 0.04690 / 3.05 ( 681) hydrogen bonds : angle 5.77124 / 4.14 ( 1923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.611 Fit side-chains REVERT: A 64 ASN cc_start: 0.7174 (m110) cc_final: 0.6888 (m110) REVERT: A 152 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7572 (ptmt) REVERT: A 212 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8100 (tpp) REVERT: A 443 ASP cc_start: 0.7821 (m-30) cc_final: 0.7362 (m-30) REVERT: B 64 ASN cc_start: 0.7208 (m110) cc_final: 0.6952 (m110) REVERT: B 104 ARG cc_start: 0.7397 (mtp85) cc_final: 0.7169 (mtp85) REVERT: B 152 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7585 (ptmt) REVERT: B 212 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8102 (tpp) REVERT: B 443 ASP cc_start: 0.7812 (m-30) cc_final: 0.7352 (m-30) REVERT: C 64 ASN cc_start: 0.7346 (m110) cc_final: 0.7005 (m110) REVERT: C 152 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7582 (ptmt) REVERT: C 212 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8100 (tpp) REVERT: C 443 ASP cc_start: 0.7820 (m-30) cc_final: 0.7347 (m-30) REVERT: D 64 ASN cc_start: 0.7314 (m110) cc_final: 0.6905 (m110) REVERT: D 212 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (tpp) REVERT: D 443 ASP cc_start: 0.7828 (m-30) cc_final: 0.7410 (m-30) outliers start: 33 outliers final: 12 residues processed: 232 average time/residue: 0.6729 time to fit residues: 171.8289 Evaluate side-chains 216 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 184 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148251 restraints weight = 18994.501| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.55 r_work: 0.3624 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16716 Z= 0.140 Angle : 0.553 5.677 22696 Z= 0.293 Chirality : 0.044 0.145 2416 Planarity : 0.005 0.046 2892 Dihedral : 11.552 89.952 2432 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.69 % Allowed : 11.74 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.09 (0.20), residues: 1944 helix: 0.68 (0.20), residues: 716 sheet: -0.99 (0.26), residues: 372 loop : 0.23 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.015 0.001 TYR C 308 PHE 0.012 0.001 PHE D 452 TRP 0.012 0.001 TRP D 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16716) covalent geometry : angle 0.55273 / 0.29 (22696) hydrogen bonds : bond 0.03674 / 2.39 ( 681) hydrogen bonds : angle 5.45627 / 3.91 ( 1923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.641 Fit side-chains REVERT: A 64 ASN cc_start: 0.7263 (m110) cc_final: 0.7023 (m110) REVERT: A 152 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7580 (ptmt) REVERT: A 212 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: A 347 GLU cc_start: 0.7792 (pm20) cc_final: 0.7423 (pm20) REVERT: A 443 ASP cc_start: 0.7841 (m-30) cc_final: 0.7431 (m-30) REVERT: A 497 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6800 (mmtp) REVERT: B 64 ASN cc_start: 0.7325 (m110) cc_final: 0.7107 (m110) REVERT: B 152 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7573 (ptmt) REVERT: B 212 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: B 347 GLU cc_start: 0.7805 (pm20) cc_final: 0.7429 (pm20) REVERT: B 443 ASP cc_start: 0.7838 (m-30) cc_final: 0.7420 (m-30) REVERT: B 497 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6801 (mmtp) REVERT: C 64 ASN cc_start: 0.7335 (m110) cc_final: 0.7060 (m110) REVERT: C 152 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7600 (ptmt) REVERT: C 212 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (tpp) REVERT: C 347 GLU cc_start: 0.7750 (pm20) cc_final: 0.7351 (pm20) REVERT: C 443 ASP cc_start: 0.7855 (m-30) cc_final: 0.7434 (m-30) REVERT: C 497 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6860 (mmtp) REVERT: D 64 ASN cc_start: 0.7464 (m110) cc_final: 0.7205 (m110) REVERT: D 212 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8116 (tpp) REVERT: D 347 GLU cc_start: 0.7745 (pm20) cc_final: 0.7340 (pm20) REVERT: D 443 ASP cc_start: 0.7849 (m-30) cc_final: 0.7433 (m-30) REVERT: D 497 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6874 (mmtp) outliers start: 29 outliers final: 10 residues processed: 231 average time/residue: 0.6283 time to fit residues: 160.8517 Evaluate side-chains 222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 95 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN C 186 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.179409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145677 restraints weight = 18869.769| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.55 r_work: 0.3593 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16716 Z= 0.198 Angle : 0.594 5.782 22696 Z= 0.314 Chirality : 0.046 0.146 2416 Planarity : 0.005 0.049 2892 Dihedral : 11.491 87.628 2432 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 12.32 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.05 (0.19), residues: 1944 helix: 0.57 (0.20), residues: 712 sheet: -0.99 (0.26), residues: 364 loop : 0.10 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 104 TYR 0.018 0.002 TYR A 308 PHE 0.014 0.002 PHE D 452 TRP 0.011 0.002 TRP C 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (16716) covalent geometry : angle 0.59420 / 0.31 (22696) hydrogen bonds : bond 0.03981 / 2.59 ( 681) hydrogen bonds : angle 5.40505 / 3.88 ( 1923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.683 Fit side-chains REVERT: A 212 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: A 347 GLU cc_start: 0.7917 (pm20) cc_final: 0.7255 (pm20) REVERT: A 443 ASP cc_start: 0.7898 (m-30) cc_final: 0.7484 (m-30) REVERT: B 152 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7638 (ptmt) REVERT: B 212 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: B 347 GLU cc_start: 0.7876 (pm20) cc_final: 0.7241 (pm20) REVERT: B 443 ASP cc_start: 0.7898 (m-30) cc_final: 0.7477 (m-30) REVERT: C 64 ASN cc_start: 0.7416 (m110) cc_final: 0.7169 (m110) REVERT: C 212 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8137 (tpp) REVERT: C 347 GLU cc_start: 0.7835 (pm20) cc_final: 0.7263 (pm20) REVERT: C 443 ASP cc_start: 0.7901 (m-30) cc_final: 0.7476 (m-30) REVERT: D 64 ASN cc_start: 0.7515 (m110) cc_final: 0.7277 (m110) REVERT: D 212 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (tpp) REVERT: D 347 GLU cc_start: 0.7814 (pm20) cc_final: 0.7243 (pm20) REVERT: D 443 ASP cc_start: 0.7896 (m-30) cc_final: 0.7476 (m-30) outliers start: 37 outliers final: 14 residues processed: 235 average time/residue: 0.6851 time to fit residues: 177.3334 Evaluate side-chains 224 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 105 ASN A 186 HIS A 307 GLN A 471 GLN B 64 ASN B 186 HIS B 307 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS C 307 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS D 307 GLN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146507 restraints weight = 18859.945| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.55 r_work: 0.3603 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16716 Z= 0.172 Angle : 0.572 5.689 22696 Z= 0.304 Chirality : 0.045 0.144 2416 Planarity : 0.005 0.048 2892 Dihedral : 11.394 88.506 2432 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 14.31 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.01 (0.19), residues: 1944 helix: 0.69 (0.20), residues: 708 sheet: -1.04 (0.26), residues: 372 loop : 0.12 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 104 TYR 0.016 0.002 TYR A 202 PHE 0.014 0.001 PHE C 452 TRP 0.012 0.002 TRP A 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16716) covalent geometry : angle 0.57224 / 0.30 (22696) hydrogen bonds : bond 0.03701 / 2.41 ( 681) hydrogen bonds : angle 5.33188 / 3.82 ( 1923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.586 Fit side-chains REVERT: A 199 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8206 (mm) REVERT: A 212 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8172 (tpp) REVERT: A 347 GLU cc_start: 0.7851 (pm20) cc_final: 0.7204 (pm20) REVERT: A 404 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7730 (ppp) REVERT: A 443 ASP cc_start: 0.7956 (m-30) cc_final: 0.7536 (m-30) REVERT: B 152 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7623 (ptmt) REVERT: B 212 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (tpp) REVERT: B 347 GLU cc_start: 0.7851 (pm20) cc_final: 0.7207 (pm20) REVERT: B 404 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7728 (ppp) REVERT: B 443 ASP cc_start: 0.7925 (m-30) cc_final: 0.7494 (m-30) REVERT: C 64 ASN cc_start: 0.7369 (m110) cc_final: 0.7126 (m110) REVERT: C 212 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8135 (tpp) REVERT: C 347 GLU cc_start: 0.7823 (pm20) cc_final: 0.7196 (pm20) REVERT: C 443 ASP cc_start: 0.7929 (m-30) cc_final: 0.7496 (m-30) REVERT: D 64 ASN cc_start: 0.7473 (m110) cc_final: 0.7219 (m110) REVERT: D 152 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7589 (ptpt) REVERT: D 212 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8128 (tpp) REVERT: D 347 GLU cc_start: 0.7834 (pm20) cc_final: 0.7205 (pm20) REVERT: D 404 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7721 (ppp) REVERT: D 443 ASP cc_start: 0.7918 (m-30) cc_final: 0.7488 (m-30) outliers start: 29 outliers final: 14 residues processed: 228 average time/residue: 0.6621 time to fit residues: 166.4907 Evaluate side-chains 223 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 105 ASN A 186 HIS ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 64 ASN B 186 HIS B 471 GLN C 105 ASN C 186 HIS C 471 GLN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.179422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145702 restraints weight = 18902.498| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.55 r_work: 0.3594 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16716 Z= 0.185 Angle : 0.584 5.751 22696 Z= 0.310 Chirality : 0.045 0.144 2416 Planarity : 0.005 0.049 2892 Dihedral : 11.378 88.040 2432 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 14.25 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.01 (0.19), residues: 1944 helix: 0.67 (0.20), residues: 708 sheet: -1.01 (0.26), residues: 364 loop : 0.07 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 104 TYR 0.017 0.002 TYR B 308 PHE 0.014 0.002 PHE A 452 TRP 0.011 0.002 TRP C 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (16716) covalent geometry : angle 0.58388 / 0.31 (22696) hydrogen bonds : bond 0.03774 / 2.46 ( 681) hydrogen bonds : angle 5.34234 / 3.83 ( 1923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.673 Fit side-chains REVERT: A 199 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 212 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8169 (tpp) REVERT: A 239 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7923 (mt-10) REVERT: A 347 GLU cc_start: 0.7901 (pm20) cc_final: 0.7197 (pm20) REVERT: A 404 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: A 443 ASP cc_start: 0.7990 (m-30) cc_final: 0.7558 (m-30) REVERT: B 212 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (tpp) REVERT: B 239 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7844 (mt-10) REVERT: B 347 GLU cc_start: 0.7893 (pm20) cc_final: 0.7197 (pm20) REVERT: B 404 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7650 (ppp) REVERT: B 443 ASP cc_start: 0.7988 (m-30) cc_final: 0.7556 (m-30) REVERT: C 64 ASN cc_start: 0.7358 (m110) cc_final: 0.7138 (m110) REVERT: C 212 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8132 (tpp) REVERT: C 239 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7850 (mt-10) REVERT: C 347 GLU cc_start: 0.7843 (pm20) cc_final: 0.7180 (pm20) REVERT: C 443 ASP cc_start: 0.7996 (m-30) cc_final: 0.7560 (m-30) REVERT: D 64 ASN cc_start: 0.7448 (m110) cc_final: 0.7233 (m110) REVERT: D 212 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8170 (tpp) REVERT: D 239 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7839 (mt-10) REVERT: D 347 GLU cc_start: 0.7802 (pm20) cc_final: 0.7128 (pm20) REVERT: D 404 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7673 (ppp) REVERT: D 443 ASP cc_start: 0.7982 (m-30) cc_final: 0.7552 (m-30) outliers start: 35 outliers final: 19 residues processed: 234 average time/residue: 0.6884 time to fit residues: 177.6034 Evaluate side-chains 232 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 186 HIS ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 64 ASN B 186 HIS B 471 GLN C 105 ASN C 186 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.180216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146606 restraints weight = 18762.037| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.54 r_work: 0.3604 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16716 Z= 0.163 Angle : 0.565 5.463 22696 Z= 0.299 Chirality : 0.044 0.143 2416 Planarity : 0.005 0.048 2892 Dihedral : 11.296 88.771 2432 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.81 % Allowed : 14.89 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.02 (0.19), residues: 1944 helix: 0.69 (0.20), residues: 712 sheet: -0.99 (0.26), residues: 364 loop : 0.08 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.016 0.002 TYR C 308 PHE 0.013 0.001 PHE C 452 TRP 0.012 0.002 TRP C 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16716) covalent geometry : angle 0.56482 / 0.30 (22696) hydrogen bonds : bond 0.03543 / 2.31 ( 681) hydrogen bonds : angle 5.29495 / 3.79 ( 1923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.695 Fit side-chains REVERT: A 212 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: A 239 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7932 (mt-10) REVERT: A 347 GLU cc_start: 0.7866 (pm20) cc_final: 0.7155 (pm20) REVERT: A 404 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7630 (ppp) REVERT: A 443 ASP cc_start: 0.7907 (m-30) cc_final: 0.7476 (m-30) REVERT: B 100 ASP cc_start: 0.6994 (t0) cc_final: 0.6536 (t0) REVERT: B 212 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (tpp) REVERT: B 239 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7900 (mt-10) REVERT: B 347 GLU cc_start: 0.7872 (pm20) cc_final: 0.7169 (pm20) REVERT: B 404 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7538 (ppp) REVERT: B 443 ASP cc_start: 0.7950 (m-30) cc_final: 0.7521 (m-30) REVERT: C 64 ASN cc_start: 0.7313 (m110) cc_final: 0.7104 (m110) REVERT: C 212 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8157 (tpp) REVERT: C 239 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7910 (mt-10) REVERT: C 347 GLU cc_start: 0.7815 (pm20) cc_final: 0.7140 (pm20) REVERT: C 443 ASP cc_start: 0.7952 (m-30) cc_final: 0.7519 (m-30) REVERT: D 64 ASN cc_start: 0.7409 (m110) cc_final: 0.7203 (m110) REVERT: D 152 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7554 (ptpt) REVERT: D 212 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: D 239 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7892 (mt-10) REVERT: D 347 GLU cc_start: 0.7780 (pm20) cc_final: 0.7102 (pm20) REVERT: D 443 ASP cc_start: 0.7909 (m-30) cc_final: 0.7471 (m-30) outliers start: 31 outliers final: 14 residues processed: 227 average time/residue: 0.7089 time to fit residues: 177.1884 Evaluate side-chains 224 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 4 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 150 optimal weight: 0.0170 chunk 53 optimal weight: 8.9990 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 105 ASN A 133 GLN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS A 384 GLN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 64 ASN B 126 ASN B 133 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS B 471 GLN C 133 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS C 426 ASN C 471 GLN D 105 ASN D 126 ASN D 133 GLN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143410 restraints weight = 18888.106| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.53 r_work: 0.3564 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16716 Z= 0.263 Angle : 0.654 5.950 22696 Z= 0.345 Chirality : 0.048 0.148 2416 Planarity : 0.005 0.050 2892 Dihedral : 11.503 85.823 2432 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 15.01 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.19 (0.19), residues: 1944 helix: 0.46 (0.20), residues: 708 sheet: -1.02 (0.26), residues: 372 loop : -0.01 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.019 0.002 TYR B 308 PHE 0.018 0.002 PHE A 452 TRP 0.010 0.002 TRP D 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (16716) covalent geometry : angle 0.65449 / 0.35 (22696) hydrogen bonds : bond 0.04332 / 2.82 ( 681) hydrogen bonds : angle 5.46769 / 3.92 ( 1923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.703 Fit side-chains REVERT: A 239 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7970 (mt-10) REVERT: A 347 GLU cc_start: 0.7975 (pm20) cc_final: 0.7229 (pm20) REVERT: A 429 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7621 (mttt) REVERT: A 443 ASP cc_start: 0.7976 (m-30) cc_final: 0.7539 (m-30) REVERT: A 474 LEU cc_start: 0.6900 (mp) cc_final: 0.6644 (tt) REVERT: B 212 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8151 (tpp) REVERT: B 239 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7914 (mt-10) REVERT: B 347 GLU cc_start: 0.7987 (pm20) cc_final: 0.7244 (pm20) REVERT: B 443 ASP cc_start: 0.7985 (m-30) cc_final: 0.7546 (m-30) REVERT: C 239 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7922 (mt-10) REVERT: C 347 GLU cc_start: 0.7970 (pm20) cc_final: 0.7213 (pm20) REVERT: C 443 ASP cc_start: 0.7981 (m-30) cc_final: 0.7488 (m-30) REVERT: D 64 ASN cc_start: 0.7416 (m110) cc_final: 0.7203 (m110) REVERT: D 212 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7983 (ttm) REVERT: D 239 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7914 (mt-10) REVERT: D 347 GLU cc_start: 0.7898 (pm20) cc_final: 0.7156 (pm20) REVERT: D 429 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7607 (mttt) REVERT: D 443 ASP cc_start: 0.7966 (m-30) cc_final: 0.7524 (m-30) REVERT: D 474 LEU cc_start: 0.6930 (mp) cc_final: 0.6696 (tt) outliers start: 29 outliers final: 17 residues processed: 235 average time/residue: 0.6605 time to fit residues: 171.1114 Evaluate side-chains 226 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 105 ASN A 133 GLN A 186 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 426 ASN A 471 GLN B 64 ASN B 133 GLN B 186 HIS B 307 GLN B 426 ASN B 471 GLN C 64 ASN C 105 ASN C 133 GLN C 186 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 133 GLN D 186 HIS D 426 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.180696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147366 restraints weight = 18899.208| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.54 r_work: 0.3614 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16716 Z= 0.138 Angle : 0.553 5.311 22696 Z= 0.293 Chirality : 0.044 0.141 2416 Planarity : 0.004 0.047 2892 Dihedral : 11.224 89.117 2432 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.29 % Allowed : 16.00 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.02 (0.19), residues: 1944 helix: 0.70 (0.20), residues: 712 sheet: -1.07 (0.26), residues: 380 loop : 0.15 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 104 TYR 0.016 0.001 TYR C 308 PHE 0.016 0.001 PHE B 66 TRP 0.015 0.001 TRP C 164 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16716) covalent geometry : angle 0.55302 / 0.29 (22696) hydrogen bonds : bond 0.03336 / 2.18 ( 681) hydrogen bonds : angle 5.29928 / 3.78 ( 1923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.665 Fit side-chains REVERT: A 239 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7933 (mt-10) REVERT: A 347 GLU cc_start: 0.7893 (pm20) cc_final: 0.7163 (pm20) REVERT: A 429 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7579 (mttt) REVERT: A 443 ASP cc_start: 0.7856 (m-30) cc_final: 0.7412 (m-30) REVERT: A 474 LEU cc_start: 0.6835 (mp) cc_final: 0.6562 (tt) REVERT: B 100 ASP cc_start: 0.6963 (t0) cc_final: 0.6467 (t0) REVERT: B 239 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7961 (mt-10) REVERT: B 347 GLU cc_start: 0.7876 (pm20) cc_final: 0.7154 (pm20) REVERT: B 443 ASP cc_start: 0.7867 (m-30) cc_final: 0.7372 (m-30) REVERT: B 497 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6884 (mmtp) REVERT: C 239 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7970 (mt-10) REVERT: C 347 GLU cc_start: 0.7837 (pm20) cc_final: 0.7141 (pm20) REVERT: C 443 ASP cc_start: 0.7874 (m-30) cc_final: 0.7421 (m-30) REVERT: D 64 ASN cc_start: 0.7317 (m110) cc_final: 0.7090 (m110) REVERT: D 152 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7552 (ptpt) REVERT: D 239 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7956 (mt-10) REVERT: D 347 GLU cc_start: 0.7872 (pm20) cc_final: 0.7180 (pm20) REVERT: D 429 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7581 (mttt) REVERT: D 443 ASP cc_start: 0.7854 (m-30) cc_final: 0.7404 (m-30) REVERT: D 497 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6891 (mmtp) outliers start: 22 outliers final: 9 residues processed: 222 average time/residue: 0.6565 time to fit residues: 160.8530 Evaluate side-chains 215 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 36 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 149 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS B 426 ASN B 471 GLN C 64 ASN C 186 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149052 restraints weight = 18784.565| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.54 r_work: 0.3634 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16716 Z= 0.119 Angle : 0.537 7.978 22696 Z= 0.283 Chirality : 0.043 0.143 2416 Planarity : 0.004 0.045 2892 Dihedral : 11.111 89.971 2432 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.05 % Allowed : 16.71 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.20), residues: 1944 helix: 0.77 (0.20), residues: 716 sheet: -1.10 (0.26), residues: 380 loop : 0.27 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 104 TYR 0.017 0.001 TYR C 308 PHE 0.017 0.001 PHE B 66 TRP 0.015 0.001 TRP C 164 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16716) covalent geometry : angle 0.53685 / 0.28 (22696) hydrogen bonds : bond 0.03087 / 2.02 ( 681) hydrogen bonds : angle 5.21926 / 3.72 ( 1923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.634 Fit side-chains REVERT: A 183 LEU cc_start: 0.7177 (tp) cc_final: 0.6873 (tt) REVERT: A 347 GLU cc_start: 0.7800 (pm20) cc_final: 0.7083 (pm20) REVERT: A 429 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7565 (mttt) REVERT: A 443 ASP cc_start: 0.7827 (m-30) cc_final: 0.7380 (m-30) REVERT: A 474 LEU cc_start: 0.6824 (mp) cc_final: 0.6544 (tt) REVERT: B 100 ASP cc_start: 0.6955 (t0) cc_final: 0.6459 (t0) REVERT: B 347 GLU cc_start: 0.7797 (pm20) cc_final: 0.7083 (pm20) REVERT: B 443 ASP cc_start: 0.7833 (m-30) cc_final: 0.7388 (m-30) REVERT: B 497 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6754 (mmtp) REVERT: C 347 GLU cc_start: 0.7769 (pm20) cc_final: 0.7085 (pm20) REVERT: C 404 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7591 (ptp) REVERT: C 443 ASP cc_start: 0.7850 (m-30) cc_final: 0.7402 (m-30) REVERT: C 497 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6742 (mmtp) REVERT: D 64 ASN cc_start: 0.7285 (m110) cc_final: 0.7071 (m110) REVERT: D 152 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7529 (ptpt) REVERT: D 347 GLU cc_start: 0.7814 (pm20) cc_final: 0.7132 (pm20) REVERT: D 443 ASP cc_start: 0.7834 (m-30) cc_final: 0.7376 (m-30) REVERT: D 474 LEU cc_start: 0.6779 (mp) cc_final: 0.6524 (tt) REVERT: D 497 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6822 (mmtp) outliers start: 18 outliers final: 7 residues processed: 218 average time/residue: 0.6416 time to fit residues: 154.5155 Evaluate side-chains 208 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 133 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS B 471 GLN C 105 ASN C 133 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS C 471 GLN D 105 ASN D 133 GLN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS D 471 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.179819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146181 restraints weight = 18704.824| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.53 r_work: 0.3598 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16716 Z= 0.178 Angle : 0.584 7.039 22696 Z= 0.308 Chirality : 0.045 0.146 2416 Planarity : 0.005 0.048 2892 Dihedral : 11.232 87.998 2432 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.23 % Allowed : 16.30 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.02 (0.19), residues: 1944 helix: 0.70 (0.20), residues: 712 sheet: -1.08 (0.26), residues: 372 loop : 0.14 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 104 TYR 0.017 0.002 TYR B 308 PHE 0.016 0.002 PHE B 66 TRP 0.010 0.002 TRP A 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (16716) covalent geometry : angle 0.58396 / 0.31 (22696) hydrogen bonds : bond 0.03611 / 2.35 ( 681) hydrogen bonds : angle 5.26682 / 3.77 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.75 seconds wall clock time: 102 minutes 58.83 seconds (6178.83 seconds total)