Starting phenix.real_space_refine on Fri Jul 3 19:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ual_26428/07_2026/7ual_26428.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 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 10220 2.51 5 N 2788 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 16164 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "C" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} Chain: "D" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3929 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 460} 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} Time building chain proxies: 3.13, per 1000 atoms: 0.19 Number of scatterers: 16164 At special positions: 0 Unit cell: (133.63, 92.96, 116.2, 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 3048 8.00 N 2788 7.00 C 10220 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: 1.02 Conformation dependent library (CDL) restraints added in 599.7 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 9 sheets defined 42.8% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.023A 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 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' 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 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.723A 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 191 removed outlier: 3.537A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.468A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.630A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.453A 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 294 removed outlier: 3.599A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 4.025A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.559A pdb=" N ARG A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 476 removed outlier: 4.002A 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 499 removed outlier: 4.079A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.323A 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 85 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' 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 127 removed outlier: 3.749A 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: 3.653A 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: 4.259A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.590A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.414A 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 315 through 320 removed outlier: 3.615A pdb=" N THR B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 4.056A pdb=" N ASP B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.876A 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 499 removed outlier: 4.062A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.315A 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 85 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' 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 Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.765A 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 189 removed outlier: 3.555A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.170A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 removed outlier: 4.293A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 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: 3.558A pdb=" N THR C 319 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.759A 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 499 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: 5.432A 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: 4.195A 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 Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.837A 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 189 removed outlier: 3.560A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 4.340A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 254 removed outlier: 3.960A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.522A pdb=" N LYS D 320 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.902A pdb=" N ASP D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.625A 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: 4.147A 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: 8.973A pdb=" N SER A 106 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 67 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 108 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY A 69 " --> pdb=" O VAL A 108 " (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: 7.295A pdb=" N ALA A 231 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG A 357 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU A 235 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY A 359 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 237 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.336A 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: 8.903A pdb=" N SER B 106 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 67 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 108 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY B 69 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 166 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.570A 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: 3.571A pdb=" N THR B 402 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B 389 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE B 373 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL B 391 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 371 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG B 393 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.149A 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: 3.775A pdb=" N ALA C 71 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 166 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.941A 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: 3.510A pdb=" N THR C 402 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 399 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE C 480 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 305 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR C 482 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 5.973A 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: 8.689A pdb=" N SER D 106 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 67 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL D 108 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY D 69 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 169 Processing sheet with id=AA9, first strand: chain 'D' and resid 415 through 423 removed outlier: 3.611A pdb=" N ALA D 399 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU D 389 " --> pdb=" O PHE D 373 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE D 373 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL D 391 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 371 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG D 393 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE D 480 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 305 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR D 482 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN D 307 " --> pdb=" O TYR D 482 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2640 1.31 - 1.43: 4580 1.43 - 1.56: 9176 1.56 - 1.69: 44 1.69 - 1.81: 132 Bond restraints: 16572 Sorted by residual: bond pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " ideal model delta sigma weight residual 1.528 1.308 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1B NAP D 602 " pdb=" C2B NAP D 602 " ideal model delta sigma weight residual 1.528 1.308 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP D 601 " pdb=" C2B NAP D 601 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 16567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 21959 2.75 - 5.49: 396 5.49 - 8.24: 87 8.24 - 10.98: 26 10.98 - 13.73: 32 Bond angle restraints: 22500 Sorted by residual: angle pdb=" N GLN C 133 " pdb=" CA GLN C 133 " pdb=" C GLN C 133 " ideal model delta sigma weight residual 112.87 105.78 7.09 1.20e+00 6.94e-01 3.49e+01 angle pdb=" N1A NAP B 602 " pdb=" C6A NAP B 602 " pdb=" N6A NAP B 602 " ideal model delta sigma weight residual 119.30 105.57 13.73 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N1A NAP C 602 " pdb=" C6A NAP C 602 " pdb=" N6A NAP C 602 " ideal model delta sigma weight residual 119.30 105.58 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N1A NAP A 602 " pdb=" C6A NAP A 602 " pdb=" N6A NAP A 602 " ideal model delta sigma weight residual 119.30 105.61 13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N1A NAP B 601 " pdb=" C6A NAP B 601 " pdb=" N6A NAP B 601 " ideal model delta sigma weight residual 119.30 105.61 13.69 3.00e+00 1.11e-01 2.08e+01 ... (remaining 22495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 8793 16.59 - 33.18: 828 33.18 - 49.77: 242 49.77 - 66.36: 51 66.36 - 82.95: 26 Dihedral angle restraints: 9940 sinusoidal: 4300 harmonic: 5640 Sorted by residual: dihedral pdb=" CA ILE C 199 " pdb=" C ILE C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP D 251 " pdb=" CB ASP D 251 " pdb=" CG ASP D 251 " pdb=" OD1 ASP D 251 " ideal model delta sinusoidal sigma weight residual -30.00 -89.64 59.64 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 251 " pdb=" CB ASP A 251 " pdb=" CG ASP A 251 " pdb=" OD1 ASP A 251 " ideal model delta sinusoidal sigma weight residual -30.00 -88.83 58.83 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 9937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2101 0.075 - 0.149: 267 0.149 - 0.223: 4 0.223 - 0.298: 8 0.298 - 0.372: 16 Chirality restraints: 2396 Sorted by residual: chirality pdb=" C2B NAP D 602 " pdb=" C1B NAP D 602 " pdb=" C3B NAP D 602 " pdb=" O2B NAP D 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C2B NAP C 602 " pdb=" C1B NAP C 602 " pdb=" C3B NAP C 602 " pdb=" O2B NAP C 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C2B NAP A 602 " pdb=" C1B NAP A 602 " pdb=" C3B NAP A 602 " pdb=" O2B NAP A 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 2393 not shown) Planarity restraints: 2868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO D 312 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 91 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 92 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 92 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.029 5.00e-02 4.00e+02 ... (remaining 2865 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1562 2.74 - 3.28: 16389 3.28 - 3.82: 28519 3.82 - 4.36: 35114 4.36 - 4.90: 58868 Nonbonded interactions: 140452 Sorted by model distance: nonbonded pdb=" OH TYR A 70 " pdb=" O GLN A 111 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG A 215 " pdb=" O MET A 273 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR D 139 " pdb=" OE1 GLU D 170 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" OE1 GLU C 94 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG B 215 " pdb=" O MET B 273 " model vdw 2.235 3.120 ... (remaining 140447 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.010 0.220 16572 Z= 0.478 Angle : 0.993 13.727 22500 Z= 0.407 Chirality : 0.055 0.372 2396 Planarity : 0.005 0.076 2868 Dihedral : 14.831 82.952 6316 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.80 % Rotamer: Outliers : 0.47 % Allowed : 0.77 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1928 helix: 0.31 (0.21), residues: 688 sheet: -1.21 (0.28), residues: 352 loop : -0.21 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 459 TYR 0.018 0.001 TYR D 139 PHE 0.012 0.001 PHE B 412 TRP 0.021 0.001 TRP D 164 HIS 0.008 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.48 (16572) covalent geometry : angle 0.99282 / 0.41 (22500) hydrogen bonds : bond 0.16752 / 10.69 ( 670) hydrogen bonds : angle 7.69447 / 5.47 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 259 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.8410 (ptmm) cc_final: 0.7841 (mmtm) REVERT: B 130 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7900 (mt) REVERT: B 261 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 37 MET cc_start: 0.7134 (mmt) cc_final: 0.6780 (mmp) REVERT: C 483 ILE cc_start: 0.7407 (mm) cc_final: 0.7174 (pt) outliers start: 8 outliers final: 3 residues processed: 266 average time/residue: 0.5229 time to fit residues: 154.4787 Evaluate side-chains 174 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 327 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN A 124 HIS A 186 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN D 430 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.147065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.122811 restraints weight = 25680.096| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.74 r_work: 0.3774 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16572 Z= 0.172 Angle : 0.655 13.435 22500 Z= 0.330 Chirality : 0.045 0.163 2396 Planarity : 0.005 0.060 2868 Dihedral : 10.084 69.007 2422 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 1.89 % Allowed : 11.08 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1928 helix: 0.35 (0.21), residues: 700 sheet: -1.15 (0.28), residues: 348 loop : -0.11 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 136 TYR 0.018 0.001 TYR D 308 PHE 0.013 0.001 PHE B 253 TRP 0.031 0.001 TRP B 462 HIS 0.012 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (16572) covalent geometry : angle 0.65514 / 0.33 (22500) hydrogen bonds : bond 0.04105 / 2.68 ( 670) hydrogen bonds : angle 6.09338 / 4.38 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: A 281 SER cc_start: 0.7595 (m) cc_final: 0.7092 (m) REVERT: A 282 ASP cc_start: 0.7836 (p0) cc_final: 0.7636 (p0) REVERT: A 368 GLU cc_start: 0.7990 (tt0) cc_final: 0.7245 (pt0) REVERT: A 411 MET cc_start: 0.8300 (mmm) cc_final: 0.8051 (mmt) REVERT: A 497 LYS cc_start: 0.8588 (ptmm) cc_final: 0.7873 (mmtm) REVERT: B 108 VAL cc_start: 0.7957 (t) cc_final: 0.7644 (m) REVERT: B 130 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7928 (mt) REVERT: B 159 MET cc_start: 0.6693 (mmt) cc_final: 0.6306 (tpt) REVERT: B 462 TRP cc_start: 0.7955 (m100) cc_final: 0.7719 (m100) REVERT: C 37 MET cc_start: 0.6853 (mmt) cc_final: 0.6620 (mmp) REVERT: C 282 ASP cc_start: 0.7275 (p0) cc_final: 0.6852 (p0) REVERT: C 286 ASP cc_start: 0.8247 (m-30) cc_final: 0.8012 (m-30) REVERT: C 456 ASP cc_start: 0.8209 (m-30) cc_final: 0.7997 (m-30) REVERT: D 411 MET cc_start: 0.8055 (tpp) cc_final: 0.7514 (mpp) outliers start: 32 outliers final: 10 residues processed: 204 average time/residue: 0.5187 time to fit residues: 117.9252 Evaluate side-chains 170 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 163 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 0.0170 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN A 124 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS C 186 HIS C 470 HIS D 430 ASN D 470 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.148139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.123932 restraints weight = 25923.434| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.73 r_work: 0.3791 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16572 Z= 0.129 Angle : 0.593 9.585 22500 Z= 0.299 Chirality : 0.043 0.148 2396 Planarity : 0.004 0.051 2868 Dihedral : 9.686 65.771 2419 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.77 % Allowed : 13.62 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1928 helix: 0.53 (0.21), residues: 700 sheet: -1.17 (0.28), residues: 348 loop : -0.05 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 459 TYR 0.014 0.001 TYR D 401 PHE 0.010 0.001 PHE C 253 TRP 0.016 0.001 TRP B 462 HIS 0.011 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16572) covalent geometry : angle 0.59293 / 0.30 (22500) hydrogen bonds : bond 0.03552 / 2.33 ( 670) hydrogen bonds : angle 5.79368 / 4.17 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 281 SER cc_start: 0.7610 (m) cc_final: 0.7106 (m) REVERT: A 282 ASP cc_start: 0.7841 (p0) cc_final: 0.7641 (p0) REVERT: A 368 GLU cc_start: 0.8037 (tt0) cc_final: 0.7281 (pt0) REVERT: A 411 MET cc_start: 0.8317 (mmm) cc_final: 0.8116 (mmt) REVERT: A 497 LYS cc_start: 0.8631 (ptmm) cc_final: 0.7884 (mmtm) REVERT: B 108 VAL cc_start: 0.7964 (t) cc_final: 0.7635 (m) REVERT: B 130 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 159 MET cc_start: 0.6702 (mmt) cc_final: 0.6308 (tpt) REVERT: B 462 TRP cc_start: 0.8010 (m100) cc_final: 0.7752 (m100) REVERT: C 282 ASP cc_start: 0.7277 (p0) cc_final: 0.6806 (p0) REVERT: C 286 ASP cc_start: 0.8233 (m-30) cc_final: 0.8002 (m-30) REVERT: D 119 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8277 (pm20) outliers start: 30 outliers final: 9 residues processed: 190 average time/residue: 0.5436 time to fit residues: 114.8805 Evaluate side-chains 173 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 13 optimal weight: 0.0770 chunk 54 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 179 optimal weight: 0.1980 chunk 191 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN A 124 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 470 HIS B 200 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS C 129 HIS D 430 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.148361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.124072 restraints weight = 25829.827| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.75 r_work: 0.3788 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16572 Z= 0.127 Angle : 0.585 8.706 22500 Z= 0.293 Chirality : 0.043 0.144 2396 Planarity : 0.004 0.049 2868 Dihedral : 9.409 60.826 2419 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 15.92 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1928 helix: 0.60 (0.21), residues: 704 sheet: -1.20 (0.28), residues: 348 loop : 0.03 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 459 TYR 0.015 0.001 TYR A 482 PHE 0.011 0.001 PHE D 413 TRP 0.010 0.001 TRP C 164 HIS 0.016 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16572) covalent geometry : angle 0.58544 / 0.29 (22500) hydrogen bonds : bond 0.03321 / 2.18 ( 670) hydrogen bonds : angle 5.67862 / 4.08 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7625 (m) cc_final: 0.7104 (m) REVERT: A 282 ASP cc_start: 0.7818 (p0) cc_final: 0.7611 (p0) REVERT: A 368 GLU cc_start: 0.8000 (tt0) cc_final: 0.7291 (pt0) REVERT: B 108 VAL cc_start: 0.7940 (t) cc_final: 0.7622 (m) REVERT: B 130 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8043 (mt) REVERT: B 159 MET cc_start: 0.6649 (mmt) cc_final: 0.6233 (tpt) REVERT: B 297 GLU cc_start: 0.7347 (pp20) cc_final: 0.7070 (pp20) REVERT: B 462 TRP cc_start: 0.8076 (m100) cc_final: 0.7822 (m100) REVERT: C 51 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7231 (m) REVERT: C 282 ASP cc_start: 0.7293 (p0) cc_final: 0.6777 (p0) REVERT: C 286 ASP cc_start: 0.8258 (m-30) cc_final: 0.7999 (m-30) REVERT: D 119 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8302 (pm20) outliers start: 28 outliers final: 14 residues processed: 192 average time/residue: 0.5153 time to fit residues: 110.1737 Evaluate side-chains 182 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.0870 chunk 124 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.145691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.121233 restraints weight = 25945.756| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.73 r_work: 0.3756 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16572 Z= 0.161 Angle : 0.604 8.235 22500 Z= 0.302 Chirality : 0.044 0.147 2396 Planarity : 0.004 0.048 2868 Dihedral : 9.308 58.947 2419 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.12 % Allowed : 15.98 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1928 helix: 0.62 (0.21), residues: 708 sheet: -1.23 (0.28), residues: 348 loop : 0.01 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 459 TYR 0.017 0.001 TYR D 308 PHE 0.011 0.001 PHE A 88 TRP 0.010 0.001 TRP C 164 HIS 0.009 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (16572) covalent geometry : angle 0.60436 / 0.30 (22500) hydrogen bonds : bond 0.03356 / 2.21 ( 670) hydrogen bonds : angle 5.58434 / 4.02 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7731 (m) cc_final: 0.7207 (m) REVERT: A 282 ASP cc_start: 0.7896 (p0) cc_final: 0.7663 (p0) REVERT: A 368 GLU cc_start: 0.8022 (tt0) cc_final: 0.7303 (pt0) REVERT: B 95 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7612 (mmtt) REVERT: B 108 VAL cc_start: 0.8047 (t) cc_final: 0.7723 (m) REVERT: B 130 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 159 MET cc_start: 0.6792 (mmt) cc_final: 0.6388 (tpt) REVERT: B 297 GLU cc_start: 0.7412 (pp20) cc_final: 0.7099 (pp20) REVERT: B 320 LYS cc_start: 0.7257 (pptt) cc_final: 0.7008 (pptt) REVERT: C 93 GLU cc_start: 0.8689 (mp0) cc_final: 0.8386 (pm20) REVERT: C 125 MET cc_start: 0.5911 (tpt) cc_final: 0.5679 (tpt) REVERT: C 282 ASP cc_start: 0.7327 (p0) cc_final: 0.6807 (p0) REVERT: C 286 ASP cc_start: 0.8277 (m-30) cc_final: 0.8017 (m-30) REVERT: D 119 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: D 457 GLU cc_start: 0.6961 (pm20) cc_final: 0.6736 (pm20) outliers start: 36 outliers final: 18 residues processed: 194 average time/residue: 0.5274 time to fit residues: 113.4038 Evaluate side-chains 182 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 86 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN B 126 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.140078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115293 restraints weight = 26499.413| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.71 r_work: 0.3673 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 16572 Z= 0.279 Angle : 0.709 9.213 22500 Z= 0.356 Chirality : 0.048 0.156 2396 Planarity : 0.005 0.052 2868 Dihedral : 9.565 60.896 2419 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 2.65 % Allowed : 16.86 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1928 helix: 0.30 (0.20), residues: 724 sheet: -1.50 (0.27), residues: 352 loop : -0.15 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 459 TYR 0.029 0.002 TYR D 308 PHE 0.020 0.002 PHE A 88 TRP 0.010 0.002 TRP C 462 HIS 0.009 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (16572) covalent geometry : angle 0.70941 / 0.36 (22500) hydrogen bonds : bond 0.04004 / 2.62 ( 670) hydrogen bonds : angle 5.72833 / 4.13 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7992 (mmt) cc_final: 0.7748 (tpt) REVERT: A 281 SER cc_start: 0.7909 (m) cc_final: 0.7356 (m) REVERT: A 282 ASP cc_start: 0.8032 (p0) cc_final: 0.7740 (p0) REVERT: A 330 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7528 (mmp80) REVERT: B 130 LEU cc_start: 0.8771 (mt) cc_final: 0.8361 (mt) REVERT: B 159 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6768 (tpt) REVERT: B 297 GLU cc_start: 0.7509 (pp20) cc_final: 0.7261 (pp20) REVERT: C 74 ARG cc_start: 0.7954 (tpm170) cc_final: 0.7638 (tpp-160) REVERT: C 214 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 282 ASP cc_start: 0.7323 (p0) cc_final: 0.6879 (p0) REVERT: C 286 ASP cc_start: 0.8327 (m-30) cc_final: 0.8074 (m-30) REVERT: D 456 ASP cc_start: 0.7746 (p0) cc_final: 0.7522 (p0) REVERT: D 457 GLU cc_start: 0.7106 (pm20) cc_final: 0.6846 (pm20) outliers start: 45 outliers final: 24 residues processed: 183 average time/residue: 0.5172 time to fit residues: 105.5539 Evaluate side-chains 177 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS C 374 HIS D 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.120262 restraints weight = 25673.477| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.72 r_work: 0.3740 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16572 Z= 0.132 Angle : 0.620 11.374 22500 Z= 0.311 Chirality : 0.044 0.140 2396 Planarity : 0.004 0.056 2868 Dihedral : 9.436 59.502 2417 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 1.95 % Allowed : 18.04 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1928 helix: 0.44 (0.21), residues: 732 sheet: -1.44 (0.28), residues: 348 loop : 0.02 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 459 TYR 0.018 0.001 TYR B 482 PHE 0.012 0.001 PHE A 88 TRP 0.011 0.001 TRP A 164 HIS 0.008 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16572) covalent geometry : angle 0.62023 / 0.31 (22500) hydrogen bonds : bond 0.03282 / 2.16 ( 670) hydrogen bonds : angle 5.59944 / 4.02 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7802 (m) cc_final: 0.7278 (m) REVERT: A 282 ASP cc_start: 0.7959 (p0) cc_final: 0.7676 (p0) REVERT: A 330 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7608 (mmp80) REVERT: A 368 GLU cc_start: 0.7918 (tt0) cc_final: 0.7090 (pt0) REVERT: B 130 LEU cc_start: 0.8704 (mt) cc_final: 0.8339 (mt) REVERT: B 159 MET cc_start: 0.6981 (mmt) cc_final: 0.6666 (tpt) REVERT: B 209 GLN cc_start: 0.8445 (mt0) cc_final: 0.8128 (mt0) REVERT: B 279 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8840 (m) REVERT: B 297 GLU cc_start: 0.7528 (pp20) cc_final: 0.7316 (pp20) REVERT: C 260 MET cc_start: 0.8559 (mtp) cc_final: 0.8358 (ttm) REVERT: C 282 ASP cc_start: 0.7359 (p0) cc_final: 0.6931 (p0) REVERT: C 286 ASP cc_start: 0.8268 (m-30) cc_final: 0.8028 (m-30) REVERT: D 79 ASP cc_start: 0.8923 (t70) cc_final: 0.8721 (t0) outliers start: 33 outliers final: 17 residues processed: 192 average time/residue: 0.5407 time to fit residues: 115.0343 Evaluate side-chains 176 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.143749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119253 restraints weight = 26007.484| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.72 r_work: 0.3724 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16572 Z= 0.162 Angle : 0.640 10.356 22500 Z= 0.321 Chirality : 0.044 0.165 2396 Planarity : 0.004 0.061 2868 Dihedral : 9.410 59.272 2417 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 1.95 % Allowed : 18.51 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1928 helix: 0.45 (0.21), residues: 732 sheet: -1.43 (0.27), residues: 348 loop : 0.02 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 459 TYR 0.018 0.001 TYR D 308 PHE 0.020 0.001 PHE B 56 TRP 0.011 0.001 TRP C 164 HIS 0.008 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (16572) covalent geometry : angle 0.64044 / 0.32 (22500) hydrogen bonds : bond 0.03294 / 2.16 ( 670) hydrogen bonds : angle 5.58205 / 4.01 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7808 (m) cc_final: 0.7280 (m) REVERT: A 282 ASP cc_start: 0.7977 (p0) cc_final: 0.7690 (p0) REVERT: A 330 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7673 (mmp80) REVERT: A 368 GLU cc_start: 0.7920 (tt0) cc_final: 0.7144 (pt0) REVERT: B 130 LEU cc_start: 0.8694 (mt) cc_final: 0.8339 (mt) REVERT: B 159 MET cc_start: 0.7014 (mmt) cc_final: 0.6703 (tpt) REVERT: B 279 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8839 (m) REVERT: B 297 GLU cc_start: 0.7518 (pp20) cc_final: 0.7294 (pp20) REVERT: C 214 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8743 (mp) REVERT: C 260 MET cc_start: 0.8590 (mtp) cc_final: 0.8386 (ttm) REVERT: C 282 ASP cc_start: 0.7360 (p0) cc_final: 0.6899 (p0) REVERT: C 286 ASP cc_start: 0.8286 (m-30) cc_final: 0.8040 (m-30) REVERT: D 404 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8326 (pp-130) outliers start: 33 outliers final: 18 residues processed: 185 average time/residue: 0.5236 time to fit residues: 107.2743 Evaluate side-chains 177 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN B 129 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117050 restraints weight = 25961.447| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.74 r_work: 0.3696 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16572 Z= 0.217 Angle : 0.693 10.922 22500 Z= 0.346 Chirality : 0.046 0.196 2396 Planarity : 0.005 0.067 2868 Dihedral : 9.548 59.173 2417 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 1.83 % Allowed : 18.69 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1928 helix: 0.30 (0.20), residues: 732 sheet: -1.52 (0.27), residues: 348 loop : -0.04 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 459 TYR 0.023 0.002 TYR D 308 PHE 0.015 0.001 PHE A 88 TRP 0.010 0.001 TRP C 164 HIS 0.009 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (16572) covalent geometry : angle 0.69309 / 0.35 (22500) hydrogen bonds : bond 0.03629 / 2.38 ( 670) hydrogen bonds : angle 5.68508 / 4.09 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7874 (m) cc_final: 0.7328 (m) REVERT: A 282 ASP cc_start: 0.8040 (p0) cc_final: 0.7728 (p0) REVERT: A 368 GLU cc_start: 0.7978 (tt0) cc_final: 0.7194 (pt0) REVERT: B 159 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6851 (tpt) REVERT: B 279 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8827 (m) REVERT: B 297 GLU cc_start: 0.7550 (pp20) cc_final: 0.7291 (pp20) REVERT: C 206 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: C 214 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8770 (mp) REVERT: C 282 ASP cc_start: 0.7340 (p0) cc_final: 0.6817 (p0) REVERT: C 286 ASP cc_start: 0.8315 (m-30) cc_final: 0.8056 (m-30) outliers start: 31 outliers final: 20 residues processed: 176 average time/residue: 0.5154 time to fit residues: 100.9842 Evaluate side-chains 178 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 174 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN B 64 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.146430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122236 restraints weight = 25618.191| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.76 r_work: 0.3758 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16572 Z= 0.126 Angle : 0.649 9.671 22500 Z= 0.325 Chirality : 0.044 0.179 2396 Planarity : 0.004 0.064 2868 Dihedral : 9.423 60.083 2417 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 19.40 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1928 helix: 0.56 (0.21), residues: 708 sheet: -1.47 (0.27), residues: 348 loop : 0.01 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 459 TYR 0.020 0.001 TYR B 482 PHE 0.017 0.001 PHE D 413 TRP 0.013 0.001 TRP A 164 HIS 0.024 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16572) covalent geometry : angle 0.64914 / 0.33 (22500) hydrogen bonds : bond 0.03129 / 2.07 ( 670) hydrogen bonds : angle 5.61792 / 4.03 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.7708 (m) cc_final: 0.7164 (m) REVERT: A 282 ASP cc_start: 0.7965 (p0) cc_final: 0.7680 (p0) REVERT: A 330 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7272 (mmp80) REVERT: A 368 GLU cc_start: 0.7936 (tt0) cc_final: 0.7123 (pt0) REVERT: B 159 MET cc_start: 0.6968 (mmt) cc_final: 0.6654 (tpt) REVERT: B 209 GLN cc_start: 0.8429 (mt0) cc_final: 0.8205 (mt0) REVERT: B 279 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8823 (m) REVERT: B 297 GLU cc_start: 0.7529 (pp20) cc_final: 0.7310 (pp20) REVERT: C 93 GLU cc_start: 0.8351 (pm20) cc_final: 0.8068 (pm20) REVERT: C 198 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8479 (mtm180) REVERT: C 214 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 282 ASP cc_start: 0.7361 (p0) cc_final: 0.6879 (p0) REVERT: C 286 ASP cc_start: 0.8242 (m-30) cc_final: 0.7997 (m-30) REVERT: D 79 ASP cc_start: 0.8940 (t70) cc_final: 0.8718 (t0) REVERT: D 119 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: D 404 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (pp-130) outliers start: 23 outliers final: 15 residues processed: 190 average time/residue: 0.5342 time to fit residues: 112.0043 Evaluate side-chains 176 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 11 optimal weight: 0.0020 chunk 81 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.143641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119589 restraints weight = 25814.143| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.72 r_work: 0.3729 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16572 Z= 0.174 Angle : 0.671 13.490 22500 Z= 0.335 Chirality : 0.045 0.186 2396 Planarity : 0.005 0.072 2868 Dihedral : 9.457 59.945 2417 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 1.42 % Allowed : 19.87 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1928 helix: 0.49 (0.21), residues: 708 sheet: -1.41 (0.28), residues: 340 loop : -0.04 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 120 TYR 0.018 0.001 TYR D 308 PHE 0.013 0.001 PHE A 88 TRP 0.010 0.001 TRP C 164 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (16572) covalent geometry : angle 0.67052 / 0.34 (22500) hydrogen bonds : bond 0.03373 / 2.20 ( 670) hydrogen bonds : angle 5.58769 / 4.02 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.54 seconds wall clock time: 66 minutes 2.06 seconds (3962.06 seconds total)