Starting phenix.real_space_refine on Fri Jul 3 07:43:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhx_61491/07_2026/9jhx_61491.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 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 8 5.49 5 S 84 5.16 5 C 8408 2.51 5 N 2156 2.21 5 O 2448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13104 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3262 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 27, 'TRANS': 382} Chain: "B" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3262 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 27, 'TRANS': 382} Chain: "C" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3262 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 27, 'TRANS': 382} Chain: "D" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3262 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 27, 'TRANS': 382} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DST': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DST': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DST': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DST': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.82, per 1000 atoms: 0.22 Number of scatterers: 13104 At special positions: 0 Unit cell: (98.4933, 105.613, 115.107, 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 84 16.00 P 8 15.00 O 2448 8.00 N 2156 7.00 C 8408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 457.6 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 4 sheets defined 51.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 38 through 58 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 137 through 151 removed outlier: 4.525A pdb=" N LYS A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.813A pdb=" N ILE A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.970A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 4.262A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 323 removed outlier: 3.923A pdb=" N ASP A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 38 through 58 Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 137 through 151 removed outlier: 4.547A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 167 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.840A pdb=" N ILE B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 220 through 237 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.607A pdb=" N LYS B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.787A pdb=" N THR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 4.095A pdb=" N SER B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.567A pdb=" N ILE B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 38 through 58 Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 62 through 76 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 137 through 151 removed outlier: 4.527A pdb=" N LYS C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 167 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.814A pdb=" N ILE C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 220 through 237 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.970A pdb=" N THR C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 4.263A pdb=" N SER C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 323 removed outlier: 3.924A pdb=" N ASP C 307 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 378 through 393 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 38 through 58 Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 137 through 151 removed outlier: 4.526A pdb=" N LYS D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 167 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.813A pdb=" N ILE D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.970A pdb=" N THR D 257 " --> pdb=" O LYS D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.263A pdb=" N SER D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 323 removed outlier: 3.924A pdb=" N ASP D 307 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 308 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 312 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 377 Processing helix chain 'D' and resid 378 through 393 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 427 through 432 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 105 current: chain 'A' and resid 114 through 121 removed outlier: 4.589A pdb=" N PHE A 117 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL A 260 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N LYS A 284 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 262 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 282 " --> pdb=" O ARG A 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 350 current: chain 'A' and resid 406 through 411 removed outlier: 3.618A pdb=" N TRP A 408 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 104 through 105 current: chain 'B' and resid 114 through 121 removed outlier: 4.544A pdb=" N PHE B 117 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL B 260 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N LYS B 284 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG B 262 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 282 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP B 268 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG B 276 " --> pdb=" O ASP B 268 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 349 through 350 current: chain 'B' and resid 406 through 411 removed outlier: 3.738A pdb=" N TRP B 408 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 104 through 105 current: chain 'C' and resid 114 through 121 removed outlier: 4.589A pdb=" N PHE C 117 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL C 260 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N LYS C 284 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG C 262 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 282 " --> pdb=" O ARG C 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 349 through 350 current: chain 'C' and resid 406 through 411 removed outlier: 3.617A pdb=" N TRP C 408 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 105 current: chain 'D' and resid 114 through 121 removed outlier: 4.590A pdb=" N PHE D 117 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N VAL D 260 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N LYS D 284 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG D 262 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 282 " --> pdb=" O ARG D 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 349 through 350 current: chain 'D' and resid 406 through 411 removed outlier: 3.618A pdb=" N TRP D 408 " --> pdb=" O TYR D 423 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1770 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: 2.02 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 4329 1.36 - 1.55: 9007 1.55 - 1.74: 8 1.74 - 1.93: 144 1.93 - 2.12: 4 Bond restraints: 13492 Sorted by residual: bond pdb=" C11 DST B 501 " pdb=" C12 DST B 501 " ideal model delta sigma weight residual 1.336 1.520 -0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C11 DST C 501 " pdb=" C12 DST C 501 " ideal model delta sigma weight residual 1.336 1.519 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C11 DST D 501 " pdb=" C12 DST D 501 " ideal model delta sigma weight residual 1.336 1.519 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" C11 DST A 501 " pdb=" C12 DST A 501 " ideal model delta sigma weight residual 1.336 1.519 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" O2 DST A 501 " pdb=" P1 DST A 501 " ideal model delta sigma weight residual 1.760 1.637 0.123 2.00e-02 2.50e+03 3.79e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 18168 3.71 - 7.42: 129 7.42 - 11.13: 41 11.13 - 14.84: 14 14.84 - 18.55: 8 Bond angle restraints: 18360 Sorted by residual: angle pdb=" N SER D 87 " pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 111.28 120.70 -9.42 1.09e+00 8.42e-01 7.47e+01 angle pdb=" N PHE C 373 " pdb=" CA PHE C 373 " pdb=" C PHE C 373 " ideal model delta sigma weight residual 111.07 101.83 9.24 1.07e+00 8.73e-01 7.45e+01 angle pdb=" N SER A 87 " pdb=" CA SER A 87 " pdb=" C SER A 87 " ideal model delta sigma weight residual 111.28 119.88 -8.60 1.09e+00 8.42e-01 6.23e+01 angle pdb=" N GLY C 377 " pdb=" CA GLY C 377 " pdb=" C GLY C 377 " ideal model delta sigma weight residual 115.63 104.05 11.58 1.49e+00 4.50e-01 6.04e+01 angle pdb=" C PHE B 84 " pdb=" N PRO B 85 " pdb=" CA PRO B 85 " ideal model delta sigma weight residual 120.23 111.53 8.70 1.23e+00 6.61e-01 5.00e+01 ... (remaining 18355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 6987 14.05 - 28.10: 794 28.10 - 42.15: 171 42.15 - 56.20: 48 56.20 - 70.25: 8 Dihedral angle restraints: 8008 sinusoidal: 3200 harmonic: 4808 Sorted by residual: dihedral pdb=" CA ALA C 105 " pdb=" C ALA C 105 " pdb=" N SER C 106 " pdb=" CA SER C 106 " ideal model delta harmonic sigma weight residual -180.00 -146.11 -33.89 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ALA A 105 " pdb=" C ALA A 105 " pdb=" N SER A 106 " pdb=" CA SER A 106 " ideal model delta harmonic sigma weight residual 180.00 -146.12 -33.88 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ALA D 105 " pdb=" C ALA D 105 " pdb=" N SER D 106 " pdb=" CA SER D 106 " ideal model delta harmonic sigma weight residual -180.00 -146.12 -33.88 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1804 0.098 - 0.197: 126 0.197 - 0.295: 11 0.295 - 0.394: 5 0.394 - 0.492: 2 Chirality restraints: 1948 Sorted by residual: chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ALA D 89 " pdb=" N ALA D 89 " pdb=" C ALA D 89 " pdb=" CB ALA D 89 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA ALA A 89 " pdb=" N ALA A 89 " pdb=" C ALA A 89 " pdb=" CB ALA A 89 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1945 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 DST D 501 " -0.045 2.00e-02 2.50e+03 1.99e-01 4.93e+02 pdb=" C11 DST D 501 " 0.183 2.00e-02 2.50e+03 pdb=" C12 DST D 501 " -0.366 2.00e-02 2.50e+03 pdb=" C13 DST D 501 " 0.141 2.00e-02 2.50e+03 pdb=" C14 DST D 501 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 DST C 501 " 0.046 2.00e-02 2.50e+03 1.99e-01 4.93e+02 pdb=" C11 DST C 501 " -0.184 2.00e-02 2.50e+03 pdb=" C12 DST C 501 " 0.366 2.00e-02 2.50e+03 pdb=" C13 DST C 501 " -0.141 2.00e-02 2.50e+03 pdb=" C14 DST C 501 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 DST A 501 " 0.045 2.00e-02 2.50e+03 1.98e-01 4.92e+02 pdb=" C11 DST A 501 " -0.183 2.00e-02 2.50e+03 pdb=" C12 DST A 501 " 0.366 2.00e-02 2.50e+03 pdb=" C13 DST A 501 " -0.141 2.00e-02 2.50e+03 pdb=" C14 DST A 501 " -0.087 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 211 2.62 - 3.19: 12657 3.19 - 3.76: 20743 3.76 - 4.33: 29681 4.33 - 4.90: 48640 Nonbonded interactions: 111932 Sorted by model distance: nonbonded pdb=" O HIS A 127 " pdb=" OG1 THR A 130 " model vdw 2.054 3.040 nonbonded pdb=" O HIS C 127 " pdb=" OG1 THR C 130 " model vdw 2.054 3.040 nonbonded pdb=" O HIS D 127 " pdb=" OG1 THR D 130 " model vdw 2.055 3.040 nonbonded pdb=" O HIS B 127 " pdb=" OG1 THR B 130 " model vdw 2.064 3.040 nonbonded pdb=" O ILE C 54 " pdb=" OG SER C 58 " model vdw 2.155 3.040 ... (remaining 111927 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: 0.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 0.184 13492 Z= 0.474 Angle : 1.070 18.555 18360 Z= 0.542 Chirality : 0.058 0.492 1948 Planarity : 0.010 0.199 2344 Dihedral : 12.822 70.254 4920 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.99 % Allowed : 6.36 % Favored : 92.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.24 (0.19), residues: 1632 helix: -2.28 (0.15), residues: 668 sheet: -1.31 (0.32), residues: 300 loop : -2.21 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 198 TYR 0.018 0.002 TYR B 264 PHE 0.038 0.002 PHE C 119 TRP 0.022 0.003 TRP B 317 HIS 0.006 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00955 / 0.47 (13492) covalent geometry : angle 1.06977 / 0.54 (18360) hydrogen bonds : bond 0.13636 / 9.40 ( 625) hydrogen bonds : angle 7.70796 / 5.56 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.487 Fit side-chains REVERT: A 110 GLN cc_start: 0.6567 (mt0) cc_final: 0.6257 (mt0) REVERT: A 119 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7554 (t80) REVERT: A 199 SER cc_start: 0.7167 (m) cc_final: 0.6711 (t) REVERT: A 234 LYS cc_start: 0.7536 (mmpt) cc_final: 0.6827 (pttp) REVERT: A 244 LYS cc_start: 0.6703 (mtmt) cc_final: 0.6497 (mtmm) REVERT: A 249 MET cc_start: 0.6697 (mtp) cc_final: 0.5901 (mtp) REVERT: A 258 MET cc_start: 0.7281 (ppp) cc_final: 0.7019 (ptt) REVERT: A 261 ASP cc_start: 0.6516 (m-30) cc_final: 0.6218 (m-30) REVERT: A 276 ARG cc_start: 0.6987 (mpp80) cc_final: 0.6632 (mtt90) REVERT: A 286 LYS cc_start: 0.7356 (tptp) cc_final: 0.7032 (tttm) REVERT: A 316 MET cc_start: 0.6653 (ttp) cc_final: 0.6322 (tpp) REVERT: B 110 GLN cc_start: 0.6912 (mt0) cc_final: 0.6530 (mt0) REVERT: B 149 GLN cc_start: 0.6878 (tp40) cc_final: 0.6590 (tp40) REVERT: B 249 MET cc_start: 0.6685 (mtp) cc_final: 0.5871 (mtp) REVERT: B 261 ASP cc_start: 0.6367 (m-30) cc_final: 0.6088 (m-30) REVERT: B 276 ARG cc_start: 0.7363 (mpp80) cc_final: 0.6728 (mtm180) REVERT: B 286 LYS cc_start: 0.7746 (tptp) cc_final: 0.7462 (tttm) REVERT: B 316 MET cc_start: 0.6759 (tmm) cc_final: 0.6482 (tpp) REVERT: C 110 GLN cc_start: 0.6607 (mt0) cc_final: 0.6315 (mt0) REVERT: C 149 GLN cc_start: 0.6748 (tp40) cc_final: 0.6436 (tp40) REVERT: C 199 SER cc_start: 0.7177 (m) cc_final: 0.6722 (t) REVERT: C 234 LYS cc_start: 0.7530 (mmpt) cc_final: 0.6815 (pttp) REVERT: C 249 MET cc_start: 0.6694 (mtp) cc_final: 0.5895 (mtp) REVERT: C 258 MET cc_start: 0.7280 (ppp) cc_final: 0.7015 (ptt) REVERT: C 261 ASP cc_start: 0.6531 (m-30) cc_final: 0.6236 (m-30) REVERT: C 276 ARG cc_start: 0.7009 (mpp80) cc_final: 0.6650 (mtt90) REVERT: C 286 LYS cc_start: 0.7354 (tptp) cc_final: 0.7033 (tttm) REVERT: C 316 MET cc_start: 0.6650 (ttp) cc_final: 0.6330 (tpp) REVERT: D 110 GLN cc_start: 0.6608 (mt0) cc_final: 0.6298 (mt0) REVERT: D 119 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7563 (t80) REVERT: D 149 GLN cc_start: 0.6736 (tp40) cc_final: 0.6421 (tp40) REVERT: D 199 SER cc_start: 0.7167 (m) cc_final: 0.6713 (t) REVERT: D 234 LYS cc_start: 0.7538 (mmpt) cc_final: 0.6820 (pttp) REVERT: D 244 LYS cc_start: 0.6756 (mtmt) cc_final: 0.6544 (mtmm) REVERT: D 249 MET cc_start: 0.6679 (mtp) cc_final: 0.5892 (mtp) REVERT: D 258 MET cc_start: 0.7280 (ppp) cc_final: 0.7010 (ptt) REVERT: D 261 ASP cc_start: 0.6497 (m-30) cc_final: 0.6201 (m-30) REVERT: D 276 ARG cc_start: 0.6990 (mpp80) cc_final: 0.6628 (mtt90) REVERT: D 286 LYS cc_start: 0.7354 (tptp) cc_final: 0.7049 (tttm) REVERT: D 316 MET cc_start: 0.6658 (ttp) cc_final: 0.6340 (tpp) outliers start: 14 outliers final: 7 residues processed: 271 average time/residue: 0.4967 time to fit residues: 147.6629 Evaluate side-chains 197 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN B 41 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167845 restraints weight = 14456.518| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.55 r_work: 0.3841 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13492 Z= 0.141 Angle : 0.629 9.183 18360 Z= 0.325 Chirality : 0.045 0.221 1948 Planarity : 0.006 0.052 2344 Dihedral : 6.546 58.898 1831 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.32 % Allowed : 13.14 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.53 (0.21), residues: 1632 helix: -0.49 (0.18), residues: 688 sheet: -0.96 (0.35), residues: 280 loop : -1.46 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.026 0.002 TYR D 264 PHE 0.017 0.002 PHE A 119 TRP 0.021 0.002 TRP B 317 HIS 0.006 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13492) covalent geometry : angle 0.62928 / 0.32 (18360) hydrogen bonds : bond 0.03988 / 2.73 ( 625) hydrogen bonds : angle 6.06504 / 4.33 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6882 (tt) REVERT: A 110 GLN cc_start: 0.6918 (mt0) cc_final: 0.6479 (mt0) REVERT: A 199 SER cc_start: 0.7159 (m) cc_final: 0.6750 (t) REVERT: A 230 GLU cc_start: 0.7468 (tp30) cc_final: 0.7088 (tp30) REVERT: A 234 LYS cc_start: 0.7183 (mmpt) cc_final: 0.6528 (pttm) REVERT: A 249 MET cc_start: 0.6694 (mtp) cc_final: 0.5806 (mtp) REVERT: A 258 MET cc_start: 0.7414 (ppp) cc_final: 0.7184 (ptt) REVERT: A 316 MET cc_start: 0.6700 (ttp) cc_final: 0.6367 (tpp) REVERT: B 110 GLN cc_start: 0.6985 (mt0) cc_final: 0.6575 (mt0) REVERT: B 149 GLN cc_start: 0.7150 (tp40) cc_final: 0.6810 (tp40) REVERT: B 199 SER cc_start: 0.6931 (OUTLIER) cc_final: 0.6379 (t) REVERT: B 247 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: B 249 MET cc_start: 0.6899 (mtp) cc_final: 0.6092 (mtp) REVERT: B 276 ARG cc_start: 0.7569 (mpp80) cc_final: 0.6942 (mtm180) REVERT: B 286 LYS cc_start: 0.7883 (tptp) cc_final: 0.7678 (tptp) REVERT: B 308 TYR cc_start: 0.6147 (m-10) cc_final: 0.5896 (m-10) REVERT: B 316 MET cc_start: 0.6856 (tmm) cc_final: 0.6453 (tpp) REVERT: C 63 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6716 (tt) REVERT: C 110 GLN cc_start: 0.6992 (mt0) cc_final: 0.6619 (mt0) REVERT: C 149 GLN cc_start: 0.7116 (tp40) cc_final: 0.6787 (tp40) REVERT: C 199 SER cc_start: 0.7173 (m) cc_final: 0.6750 (t) REVERT: C 234 LYS cc_start: 0.7160 (mmpt) cc_final: 0.6692 (pttm) REVERT: C 249 MET cc_start: 0.6629 (mtp) cc_final: 0.5736 (mtp) REVERT: C 258 MET cc_start: 0.7487 (ppp) cc_final: 0.7253 (ptt) REVERT: C 316 MET cc_start: 0.6756 (ttp) cc_final: 0.6422 (tpp) REVERT: D 63 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6877 (tt) REVERT: D 110 GLN cc_start: 0.6917 (mt0) cc_final: 0.6543 (mt0) REVERT: D 199 SER cc_start: 0.7176 (m) cc_final: 0.6762 (t) REVERT: D 230 GLU cc_start: 0.7285 (tp30) cc_final: 0.6975 (tp30) REVERT: D 234 LYS cc_start: 0.7133 (mmpt) cc_final: 0.6496 (pttm) REVERT: D 249 MET cc_start: 0.6696 (mtp) cc_final: 0.5786 (mtp) REVERT: D 258 MET cc_start: 0.7447 (ppp) cc_final: 0.7211 (ptt) REVERT: D 316 MET cc_start: 0.6766 (ttp) cc_final: 0.6427 (tpp) outliers start: 47 outliers final: 20 residues processed: 270 average time/residue: 0.4953 time to fit residues: 147.8108 Evaluate side-chains 234 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164247 restraints weight = 14704.977| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.57 r_work: 0.3809 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13492 Z= 0.196 Angle : 0.677 7.921 18360 Z= 0.345 Chirality : 0.046 0.277 1948 Planarity : 0.006 0.047 2344 Dihedral : 6.420 51.824 1831 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.88 % Allowed : 17.09 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.92 (0.22), residues: 1632 helix: 0.06 (0.20), residues: 660 sheet: -0.83 (0.35), residues: 280 loop : -1.05 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.024 0.002 TYR D 264 PHE 0.018 0.002 PHE A 119 TRP 0.022 0.002 TRP B 317 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (13492) covalent geometry : angle 0.67658 / 0.35 (18360) hydrogen bonds : bond 0.04250 / 2.90 ( 625) hydrogen bonds : angle 6.05241 / 4.33 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6724 (tt) REVERT: A 110 GLN cc_start: 0.6987 (mt0) cc_final: 0.6573 (mt0) REVERT: A 197 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6500 (mp10) REVERT: A 199 SER cc_start: 0.7351 (m) cc_final: 0.6891 (t) REVERT: A 221 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6422 (mmm) REVERT: A 230 GLU cc_start: 0.7115 (tp30) cc_final: 0.6754 (tp30) REVERT: A 234 LYS cc_start: 0.7093 (mmpt) cc_final: 0.6064 (mtmm) REVERT: A 249 MET cc_start: 0.6828 (mtp) cc_final: 0.5999 (mtp) REVERT: A 286 LYS cc_start: 0.7709 (tptp) cc_final: 0.7186 (ttpp) REVERT: A 316 MET cc_start: 0.6861 (ttp) cc_final: 0.6494 (tpp) REVERT: A 318 ASP cc_start: 0.5557 (t0) cc_final: 0.5343 (m-30) REVERT: A 320 ILE cc_start: 0.7083 (tt) cc_final: 0.6847 (mp) REVERT: B 110 GLN cc_start: 0.6962 (mt0) cc_final: 0.6557 (mt0) REVERT: B 199 SER cc_start: 0.7029 (OUTLIER) cc_final: 0.6401 (t) REVERT: B 217 MET cc_start: 0.8325 (mtt) cc_final: 0.8109 (mmt) REVERT: B 221 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6400 (mmm) REVERT: B 230 GLU cc_start: 0.7332 (tp30) cc_final: 0.6861 (tp30) REVERT: B 249 MET cc_start: 0.6898 (mtp) cc_final: 0.6022 (mtp) REVERT: B 276 ARG cc_start: 0.7603 (mpp80) cc_final: 0.7035 (mtm180) REVERT: B 286 LYS cc_start: 0.7872 (tptp) cc_final: 0.7660 (tptp) REVERT: B 300 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6475 (mtt180) REVERT: B 316 MET cc_start: 0.7016 (tmm) cc_final: 0.6522 (tpp) REVERT: C 63 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6717 (tt) REVERT: C 110 GLN cc_start: 0.7064 (mt0) cc_final: 0.6526 (mt0) REVERT: C 197 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: C 199 SER cc_start: 0.7357 (m) cc_final: 0.6889 (t) REVERT: C 221 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6443 (mmm) REVERT: C 230 GLU cc_start: 0.7229 (tp30) cc_final: 0.6956 (tp30) REVERT: C 234 LYS cc_start: 0.7024 (mmpt) cc_final: 0.6780 (ttpp) REVERT: C 249 MET cc_start: 0.6806 (mtp) cc_final: 0.6005 (mtp) REVERT: C 276 ARG cc_start: 0.7110 (mpp80) cc_final: 0.6583 (mpp80) REVERT: C 286 LYS cc_start: 0.7675 (tptp) cc_final: 0.7213 (ttpp) REVERT: C 316 MET cc_start: 0.6883 (ttp) cc_final: 0.6525 (tpp) REVERT: C 320 ILE cc_start: 0.7095 (tt) cc_final: 0.6854 (mp) REVERT: D 63 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6728 (tt) REVERT: D 110 GLN cc_start: 0.6988 (mt0) cc_final: 0.6586 (mt0) REVERT: D 149 GLN cc_start: 0.6898 (tp40) cc_final: 0.6606 (tp40) REVERT: D 197 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6498 (mp10) REVERT: D 199 SER cc_start: 0.7381 (m) cc_final: 0.6924 (t) REVERT: D 217 MET cc_start: 0.8373 (mtt) cc_final: 0.8164 (mmt) REVERT: D 221 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6458 (mmm) REVERT: D 230 GLU cc_start: 0.7147 (tp30) cc_final: 0.6715 (tp30) REVERT: D 234 LYS cc_start: 0.7096 (mmpt) cc_final: 0.6023 (mtmm) REVERT: D 249 MET cc_start: 0.6856 (mtp) cc_final: 0.6016 (mtp) REVERT: D 286 LYS cc_start: 0.7675 (tptp) cc_final: 0.7187 (ttpp) REVERT: D 316 MET cc_start: 0.6884 (ttp) cc_final: 0.6531 (tpp) REVERT: D 318 ASP cc_start: 0.5590 (t0) cc_final: 0.5370 (m-30) REVERT: D 320 ILE cc_start: 0.7071 (tt) cc_final: 0.6847 (mp) outliers start: 55 outliers final: 25 residues processed: 255 average time/residue: 0.5141 time to fit residues: 144.7292 Evaluate side-chains 240 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.197128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.169642 restraints weight = 14646.403| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.55 r_work: 0.3856 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13492 Z= 0.120 Angle : 0.585 7.474 18360 Z= 0.297 Chirality : 0.043 0.252 1948 Planarity : 0.005 0.048 2344 Dihedral : 5.706 35.426 1827 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.67 % Allowed : 19.21 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.22), residues: 1632 helix: 0.48 (0.20), residues: 660 sheet: -0.74 (0.34), residues: 312 loop : -0.61 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 118 TYR 0.019 0.002 TYR B 264 PHE 0.012 0.001 PHE A 226 TRP 0.021 0.001 TRP B 317 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13492) covalent geometry : angle 0.58523 / 0.30 (18360) hydrogen bonds : bond 0.03317 / 2.27 ( 625) hydrogen bonds : angle 5.61720 / 4.01 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6847 (mt0) cc_final: 0.6399 (mt0) REVERT: A 116 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6142 (mmt) REVERT: A 199 SER cc_start: 0.7250 (m) cc_final: 0.6797 (t) REVERT: A 221 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6329 (mmm) REVERT: A 230 GLU cc_start: 0.7115 (tp30) cc_final: 0.6786 (tp30) REVERT: A 234 LYS cc_start: 0.6883 (mmpt) cc_final: 0.6134 (mtmm) REVERT: A 249 MET cc_start: 0.6559 (mtp) cc_final: 0.5891 (mtp) REVERT: A 286 LYS cc_start: 0.7833 (tptp) cc_final: 0.7215 (ttpp) REVERT: A 308 TYR cc_start: 0.5833 (m-10) cc_final: 0.5612 (m-10) REVERT: B 110 GLN cc_start: 0.6712 (mt0) cc_final: 0.6298 (mt0) REVERT: B 199 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6435 (t) REVERT: B 221 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6319 (mmm) REVERT: B 230 GLU cc_start: 0.7178 (tp30) cc_final: 0.6800 (tp30) REVERT: B 249 MET cc_start: 0.6763 (mtp) cc_final: 0.5774 (mtp) REVERT: B 259 MET cc_start: 0.6194 (ptp) cc_final: 0.5087 (ttp) REVERT: B 276 ARG cc_start: 0.7498 (mpp80) cc_final: 0.6965 (mtm180) REVERT: B 300 ARG cc_start: 0.6719 (mtt90) cc_final: 0.6369 (mtt180) REVERT: B 308 TYR cc_start: 0.6035 (m-10) cc_final: 0.5814 (m-10) REVERT: B 316 MET cc_start: 0.7063 (tmm) cc_final: 0.6560 (tpp) REVERT: C 110 GLN cc_start: 0.6899 (mt0) cc_final: 0.6513 (mt0) REVERT: C 116 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6344 (mmt) REVERT: C 199 SER cc_start: 0.7217 (m) cc_final: 0.6745 (t) REVERT: C 221 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6334 (mmm) REVERT: C 230 GLU cc_start: 0.7224 (tp30) cc_final: 0.6936 (tp30) REVERT: C 249 MET cc_start: 0.6545 (mtp) cc_final: 0.5887 (mtp) REVERT: C 286 LYS cc_start: 0.7805 (tptp) cc_final: 0.7228 (ttpp) REVERT: C 308 TYR cc_start: 0.5877 (m-10) cc_final: 0.5653 (m-10) REVERT: D 110 GLN cc_start: 0.6847 (mt0) cc_final: 0.6407 (mt0) REVERT: D 116 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6183 (mmt) REVERT: D 199 SER cc_start: 0.7275 (m) cc_final: 0.6823 (t) REVERT: D 221 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6351 (mmm) REVERT: D 230 GLU cc_start: 0.7121 (tp30) cc_final: 0.6877 (tp30) REVERT: D 234 LYS cc_start: 0.6884 (mmpt) cc_final: 0.6563 (ttpp) REVERT: D 249 MET cc_start: 0.6568 (mtp) cc_final: 0.5892 (mtp) REVERT: D 286 LYS cc_start: 0.7807 (tptp) cc_final: 0.7230 (ttpp) REVERT: D 308 TYR cc_start: 0.5885 (m-10) cc_final: 0.5670 (m-10) outliers start: 52 outliers final: 18 residues processed: 245 average time/residue: 0.4927 time to fit residues: 133.1590 Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.196496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169112 restraints weight = 14766.194| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.55 r_work: 0.3855 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13492 Z= 0.135 Angle : 0.609 7.488 18360 Z= 0.307 Chirality : 0.043 0.234 1948 Planarity : 0.006 0.071 2344 Dihedral : 5.683 40.293 1827 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.74 % Allowed : 19.70 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1632 helix: 0.61 (0.20), residues: 664 sheet: -0.67 (0.35), residues: 280 loop : -0.75 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.021 0.002 TYR C 264 PHE 0.012 0.001 PHE C 226 TRP 0.020 0.001 TRP B 317 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13492) covalent geometry : angle 0.60890 / 0.31 (18360) hydrogen bonds : bond 0.03490 / 2.38 ( 625) hydrogen bonds : angle 5.57881 / 3.98 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6804 (mt0) cc_final: 0.6271 (mt0) REVERT: A 199 SER cc_start: 0.7214 (m) cc_final: 0.6761 (t) REVERT: A 221 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6365 (mmm) REVERT: A 230 GLU cc_start: 0.7187 (tp30) cc_final: 0.6847 (tp30) REVERT: A 234 LYS cc_start: 0.6777 (mmpt) cc_final: 0.5983 (mtmm) REVERT: A 245 ILE cc_start: 0.7749 (mt) cc_final: 0.7502 (mt) REVERT: A 247 GLU cc_start: 0.6332 (mt-10) cc_final: 0.6054 (mt-10) REVERT: A 249 MET cc_start: 0.6587 (mtp) cc_final: 0.5951 (mtp) REVERT: A 286 LYS cc_start: 0.7864 (tptp) cc_final: 0.7563 (tptp) REVERT: B 110 GLN cc_start: 0.6658 (mt0) cc_final: 0.6289 (mt0) REVERT: B 197 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: B 199 SER cc_start: 0.6890 (OUTLIER) cc_final: 0.6340 (t) REVERT: B 221 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6266 (mmm) REVERT: B 230 GLU cc_start: 0.7220 (tp30) cc_final: 0.6923 (tp30) REVERT: B 249 MET cc_start: 0.6788 (mtp) cc_final: 0.5962 (mtp) REVERT: B 259 MET cc_start: 0.6245 (ptp) cc_final: 0.5140 (ttp) REVERT: B 276 ARG cc_start: 0.7486 (mpp80) cc_final: 0.6988 (mtm180) REVERT: B 286 LYS cc_start: 0.7586 (tptp) cc_final: 0.7099 (ttpp) REVERT: B 308 TYR cc_start: 0.6203 (m-10) cc_final: 0.5994 (m-10) REVERT: B 316 MET cc_start: 0.6967 (tmm) cc_final: 0.6670 (tpp) REVERT: C 110 GLN cc_start: 0.6584 (mt0) cc_final: 0.6118 (mt0) REVERT: C 122 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 197 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6403 (mp10) REVERT: C 199 SER cc_start: 0.7215 (m) cc_final: 0.6738 (t) REVERT: C 221 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6354 (mmm) REVERT: C 230 GLU cc_start: 0.7358 (tp30) cc_final: 0.7003 (tp30) REVERT: C 249 MET cc_start: 0.6585 (mtp) cc_final: 0.5933 (mtp) REVERT: C 286 LYS cc_start: 0.7819 (tptp) cc_final: 0.7531 (tptp) REVERT: C 308 TYR cc_start: 0.5790 (m-10) cc_final: 0.5586 (m-10) REVERT: D 110 GLN cc_start: 0.6811 (mt0) cc_final: 0.6301 (mt0) REVERT: D 199 SER cc_start: 0.7239 (m) cc_final: 0.6785 (t) REVERT: D 221 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6361 (mmm) REVERT: D 234 LYS cc_start: 0.6746 (mmpt) cc_final: 0.6138 (mtmm) REVERT: D 245 ILE cc_start: 0.7735 (mt) cc_final: 0.7489 (mt) REVERT: D 247 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6039 (mt-10) REVERT: D 249 MET cc_start: 0.6590 (mtp) cc_final: 0.5883 (mtp) REVERT: D 286 LYS cc_start: 0.7824 (tptp) cc_final: 0.7532 (tptp) outliers start: 53 outliers final: 22 residues processed: 260 average time/residue: 0.4802 time to fit residues: 137.9157 Evaluate side-chains 239 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 127 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 ASN C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.199328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172311 restraints weight = 14729.191| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.57 r_work: 0.3889 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13492 Z= 0.113 Angle : 0.591 9.408 18360 Z= 0.298 Chirality : 0.043 0.226 1948 Planarity : 0.005 0.072 2344 Dihedral : 5.416 44.920 1827 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.38 % Allowed : 20.62 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1632 helix: 0.75 (0.20), residues: 664 sheet: -0.78 (0.34), residues: 308 loop : -0.45 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 276 TYR 0.019 0.001 TYR A 264 PHE 0.011 0.001 PHE C 226 TRP 0.018 0.001 TRP B 317 HIS 0.003 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13492) covalent geometry : angle 0.59095 / 0.30 (18360) hydrogen bonds : bond 0.03130 / 2.13 ( 625) hydrogen bonds : angle 5.34350 / 3.80 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6509 (mt0) cc_final: 0.5969 (mt0) REVERT: A 116 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6346 (mmt) REVERT: A 122 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: A 199 SER cc_start: 0.7136 (m) cc_final: 0.6663 (t) REVERT: A 234 LYS cc_start: 0.6683 (mmpt) cc_final: 0.6137 (mtmm) REVERT: A 245 ILE cc_start: 0.7572 (mt) cc_final: 0.7327 (mt) REVERT: A 247 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6054 (mt-10) REVERT: A 286 LYS cc_start: 0.7815 (tptp) cc_final: 0.7606 (tptp) REVERT: A 308 TYR cc_start: 0.5650 (m-10) cc_final: 0.5354 (m-10) REVERT: A 311 LYS cc_start: 0.6258 (tptp) cc_final: 0.5155 (ptpt) REVERT: B 110 GLN cc_start: 0.6658 (mt0) cc_final: 0.6235 (mt0) REVERT: B 197 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6466 (mp10) REVERT: B 199 SER cc_start: 0.7072 (OUTLIER) cc_final: 0.6533 (t) REVERT: B 221 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6236 (mmm) REVERT: B 249 MET cc_start: 0.6780 (mtp) cc_final: 0.6078 (mtp) REVERT: B 259 MET cc_start: 0.6308 (ptp) cc_final: 0.5167 (ttp) REVERT: B 286 LYS cc_start: 0.7584 (tptp) cc_final: 0.7347 (tptp) REVERT: B 316 MET cc_start: 0.6918 (tmm) cc_final: 0.6678 (tpp) REVERT: C 110 GLN cc_start: 0.6430 (mt0) cc_final: 0.5966 (mt0) REVERT: C 116 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6225 (mmt) REVERT: C 199 SER cc_start: 0.7133 (m) cc_final: 0.6670 (t) REVERT: C 230 GLU cc_start: 0.7366 (tp30) cc_final: 0.6953 (tp30) REVERT: C 245 ILE cc_start: 0.7513 (mt) cc_final: 0.7252 (mt) REVERT: C 247 GLU cc_start: 0.6288 (mt-10) cc_final: 0.5953 (mt-10) REVERT: C 286 LYS cc_start: 0.7804 (tptp) cc_final: 0.7603 (tptp) REVERT: C 308 TYR cc_start: 0.5987 (m-10) cc_final: 0.5769 (m-10) REVERT: C 311 LYS cc_start: 0.6296 (tptp) cc_final: 0.5178 (ptpt) REVERT: D 110 GLN cc_start: 0.6517 (mt0) cc_final: 0.5983 (mt0) REVERT: D 116 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6357 (mmt) REVERT: D 122 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: D 199 SER cc_start: 0.7151 (m) cc_final: 0.6691 (t) REVERT: D 245 ILE cc_start: 0.7506 (mt) cc_final: 0.7261 (mt) REVERT: D 247 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6126 (mt-10) REVERT: D 286 LYS cc_start: 0.7782 (tptp) cc_final: 0.7538 (tptp) REVERT: D 308 TYR cc_start: 0.5682 (m-10) cc_final: 0.5408 (m-10) REVERT: D 311 LYS cc_start: 0.6246 (tptp) cc_final: 0.5159 (ptpt) outliers start: 62 outliers final: 20 residues processed: 253 average time/residue: 0.4608 time to fit residues: 129.6897 Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 7 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 162 optimal weight: 0.0020 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 334 ASN D 108 ASN D 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167427 restraints weight = 14712.915| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.53 r_work: 0.3839 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13492 Z= 0.170 Angle : 0.656 9.873 18360 Z= 0.331 Chirality : 0.045 0.247 1948 Planarity : 0.006 0.074 2344 Dihedral : 5.756 51.386 1827 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.18 % Allowed : 23.02 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.22), residues: 1632 helix: 0.71 (0.20), residues: 664 sheet: -0.68 (0.35), residues: 280 loop : -0.52 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 276 TYR 0.023 0.002 TYR A 264 PHE 0.014 0.002 PHE D 226 TRP 0.018 0.002 TRP B 317 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13492) covalent geometry : angle 0.65559 / 0.33 (18360) hydrogen bonds : bond 0.03812 / 2.58 ( 625) hydrogen bonds : angle 5.72709 / 4.08 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6772 (mt0) cc_final: 0.6248 (mt0) REVERT: A 122 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 199 SER cc_start: 0.7223 (m) cc_final: 0.6749 (t) REVERT: A 221 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6332 (mmm) REVERT: A 234 LYS cc_start: 0.6865 (mmpt) cc_final: 0.6309 (mtmm) REVERT: A 245 ILE cc_start: 0.7719 (mt) cc_final: 0.7501 (mt) REVERT: A 247 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6078 (mt-10) REVERT: A 286 LYS cc_start: 0.7810 (tptp) cc_final: 0.7559 (tptp) REVERT: A 308 TYR cc_start: 0.5684 (m-10) cc_final: 0.5469 (m-10) REVERT: B 110 GLN cc_start: 0.6704 (mt0) cc_final: 0.6275 (mt0) REVERT: B 197 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6555 (mp10) REVERT: B 199 SER cc_start: 0.6969 (OUTLIER) cc_final: 0.6409 (t) REVERT: B 221 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6145 (mmm) REVERT: B 249 MET cc_start: 0.6836 (mtp) cc_final: 0.6068 (mtp) REVERT: B 259 MET cc_start: 0.6492 (ptp) cc_final: 0.5350 (ttp) REVERT: B 276 ARG cc_start: 0.7440 (mpp80) cc_final: 0.6971 (mtm180) REVERT: C 110 GLN cc_start: 0.6488 (mt0) cc_final: 0.6010 (mt0) REVERT: C 122 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: C 199 SER cc_start: 0.7232 (m) cc_final: 0.6767 (t) REVERT: C 221 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6325 (mmm) REVERT: C 230 GLU cc_start: 0.7412 (tp30) cc_final: 0.7026 (tp30) REVERT: C 245 ILE cc_start: 0.7644 (mt) cc_final: 0.7403 (mt) REVERT: C 247 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5983 (mt-10) REVERT: C 258 MET cc_start: 0.6926 (ptt) cc_final: 0.6693 (ptt) REVERT: C 286 LYS cc_start: 0.7769 (tptp) cc_final: 0.7533 (tptp) REVERT: C 308 TYR cc_start: 0.5899 (m-10) cc_final: 0.5679 (m-10) REVERT: D 110 GLN cc_start: 0.6641 (mt0) cc_final: 0.6117 (mt0) REVERT: D 122 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: D 199 SER cc_start: 0.7254 (m) cc_final: 0.6781 (t) REVERT: D 221 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6247 (mmm) REVERT: D 230 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7083 (tp30) REVERT: D 245 ILE cc_start: 0.7681 (mt) cc_final: 0.7448 (mt) REVERT: D 247 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6077 (mt-10) REVERT: D 258 MET cc_start: 0.7020 (ptt) cc_final: 0.6799 (ptt) REVERT: D 286 LYS cc_start: 0.7752 (tptp) cc_final: 0.7495 (tptp) REVERT: D 308 TYR cc_start: 0.5660 (m-10) cc_final: 0.5381 (m-10) REVERT: D 311 LYS cc_start: 0.6280 (tptp) cc_final: 0.5208 (ptmt) outliers start: 45 outliers final: 24 residues processed: 247 average time/residue: 0.5122 time to fit residues: 139.9654 Evaluate side-chains 242 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 88 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.199408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172887 restraints weight = 14644.662| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.53 r_work: 0.3896 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13492 Z= 0.116 Angle : 0.598 9.706 18360 Z= 0.301 Chirality : 0.043 0.263 1948 Planarity : 0.006 0.076 2344 Dihedral : 5.528 59.325 1827 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.32 % Allowed : 23.31 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1632 helix: 0.83 (0.20), residues: 664 sheet: -0.62 (0.34), residues: 312 loop : -0.16 (0.28), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 276 TYR 0.019 0.001 TYR C 264 PHE 0.011 0.001 PHE D 226 TRP 0.017 0.001 TRP B 317 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13492) covalent geometry : angle 0.59800 / 0.30 (18360) hydrogen bonds : bond 0.03128 / 2.12 ( 625) hydrogen bonds : angle 5.39943 / 3.85 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6408 (mt0) cc_final: 0.5842 (mt0) REVERT: A 122 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 199 SER cc_start: 0.7098 (m) cc_final: 0.6645 (t) REVERT: A 234 LYS cc_start: 0.6798 (mmpt) cc_final: 0.6255 (mtmm) REVERT: A 247 GLU cc_start: 0.6215 (mt-10) cc_final: 0.5931 (mt-10) REVERT: A 286 LYS cc_start: 0.7661 (tptp) cc_final: 0.7456 (tptp) REVERT: A 308 TYR cc_start: 0.5965 (m-10) cc_final: 0.5753 (m-10) REVERT: B 110 GLN cc_start: 0.6620 (mt0) cc_final: 0.6180 (mt0) REVERT: B 197 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6490 (mp10) REVERT: B 199 SER cc_start: 0.7126 (OUTLIER) cc_final: 0.6574 (t) REVERT: B 221 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6022 (mmm) REVERT: B 249 MET cc_start: 0.6765 (mtp) cc_final: 0.6026 (mtp) REVERT: B 259 MET cc_start: 0.6445 (ptp) cc_final: 0.5385 (ttp) REVERT: B 261 ASP cc_start: 0.6957 (m-30) cc_final: 0.6554 (m-30) REVERT: B 286 LYS cc_start: 0.7234 (tptp) cc_final: 0.6716 (ttpp) REVERT: B 325 LEU cc_start: 0.7312 (tt) cc_final: 0.7089 (tm) REVERT: C 110 GLN cc_start: 0.6252 (mt0) cc_final: 0.5831 (mt0) REVERT: C 116 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.5810 (mmt) REVERT: C 121 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6930 (pt) REVERT: C 199 SER cc_start: 0.7119 (m) cc_final: 0.6685 (t) REVERT: C 221 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6335 (mmm) REVERT: C 230 GLU cc_start: 0.7355 (tp30) cc_final: 0.7134 (tp30) REVERT: C 247 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5937 (mt-10) REVERT: C 258 MET cc_start: 0.6687 (ptt) cc_final: 0.6419 (ptt) REVERT: D 122 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: D 197 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6314 (mp10) REVERT: D 199 SER cc_start: 0.7149 (m) cc_final: 0.6674 (t) REVERT: D 221 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6332 (mmm) REVERT: D 230 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: D 247 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5947 (mt-10) REVERT: D 258 MET cc_start: 0.6914 (ptt) cc_final: 0.6672 (ptt) REVERT: D 286 LYS cc_start: 0.7586 (tptp) cc_final: 0.7359 (tptp) REVERT: D 308 TYR cc_start: 0.5957 (m-10) cc_final: 0.5750 (m-10) outliers start: 47 outliers final: 24 residues processed: 242 average time/residue: 0.4880 time to fit residues: 130.9084 Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 154 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.198776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172365 restraints weight = 14655.218| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.52 r_work: 0.3880 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13492 Z= 0.123 Angle : 0.613 9.798 18360 Z= 0.308 Chirality : 0.044 0.268 1948 Planarity : 0.005 0.078 2344 Dihedral : 5.527 57.217 1827 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.53 % Allowed : 22.88 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1632 helix: 0.89 (0.20), residues: 664 sheet: -0.59 (0.34), residues: 312 loop : -0.14 (0.28), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 276 TYR 0.020 0.002 TYR D 264 PHE 0.020 0.001 PHE D 226 TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13492) covalent geometry : angle 0.61343 / 0.31 (18360) hydrogen bonds : bond 0.03228 / 2.18 ( 625) hydrogen bonds : angle 5.38719 / 3.84 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6386 (mt0) cc_final: 0.5869 (mt0) REVERT: A 122 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 199 SER cc_start: 0.7099 (m) cc_final: 0.6648 (t) REVERT: A 234 LYS cc_start: 0.6807 (mmpt) cc_final: 0.6291 (mtmm) REVERT: A 247 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5964 (mt-10) REVERT: A 308 TYR cc_start: 0.5997 (m-10) cc_final: 0.5788 (m-10) REVERT: A 311 LYS cc_start: 0.6073 (tptp) cc_final: 0.4780 (ptpt) REVERT: B 81 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: B 110 GLN cc_start: 0.6590 (mt0) cc_final: 0.6172 (mt0) REVERT: B 199 SER cc_start: 0.7035 (OUTLIER) cc_final: 0.6526 (t) REVERT: B 221 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6106 (mmm) REVERT: B 249 MET cc_start: 0.6807 (mtp) cc_final: 0.6131 (mtp) REVERT: B 259 MET cc_start: 0.6472 (ptp) cc_final: 0.5416 (ttp) REVERT: B 261 ASP cc_start: 0.6921 (m-30) cc_final: 0.6525 (m-30) REVERT: B 286 LYS cc_start: 0.7274 (tptp) cc_final: 0.6724 (ttpp) REVERT: B 325 LEU cc_start: 0.7301 (tt) cc_final: 0.7010 (tm) REVERT: B 410 SER cc_start: 0.6703 (t) cc_final: 0.6469 (p) REVERT: C 110 GLN cc_start: 0.6092 (mt0) cc_final: 0.5662 (mt0) REVERT: C 116 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.5769 (mmt) REVERT: C 122 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: C 199 SER cc_start: 0.7109 (m) cc_final: 0.6671 (t) REVERT: C 221 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6360 (mmm) REVERT: C 230 GLU cc_start: 0.7356 (tp30) cc_final: 0.6907 (tp30) REVERT: C 247 GLU cc_start: 0.6269 (mt-10) cc_final: 0.6017 (mt-10) REVERT: C 258 MET cc_start: 0.6658 (ptt) cc_final: 0.6400 (ptt) REVERT: C 286 LYS cc_start: 0.7422 (tptp) cc_final: 0.6986 (ttpp) REVERT: C 308 TYR cc_start: 0.5889 (m-10) cc_final: 0.5641 (m-10) REVERT: D 110 GLN cc_start: 0.6440 (mt0) cc_final: 0.5953 (mt0) REVERT: D 116 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6330 (mmt) REVERT: D 122 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: D 197 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6350 (mp10) REVERT: D 199 SER cc_start: 0.7070 (m) cc_final: 0.6593 (t) REVERT: D 221 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6367 (mmm) REVERT: D 230 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: D 247 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5841 (mt-10) REVERT: D 258 MET cc_start: 0.6888 (ptt) cc_final: 0.6649 (ptt) REVERT: D 286 LYS cc_start: 0.7599 (tptp) cc_final: 0.7398 (tptp) outliers start: 50 outliers final: 30 residues processed: 240 average time/residue: 0.4704 time to fit residues: 125.2613 Evaluate side-chains 244 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 142 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.200038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173778 restraints weight = 14780.290| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.53 r_work: 0.3900 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13492 Z= 0.120 Angle : 0.616 9.787 18360 Z= 0.309 Chirality : 0.043 0.262 1948 Planarity : 0.006 0.079 2344 Dihedral : 5.535 56.746 1827 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.60 % Allowed : 23.23 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1632 helix: 0.91 (0.20), residues: 664 sheet: -0.79 (0.33), residues: 328 loop : 0.04 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.019 0.001 TYR C 264 PHE 0.019 0.001 PHE D 226 TRP 0.018 0.001 TRP B 317 HIS 0.003 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13492) covalent geometry : angle 0.61550 / 0.31 (18360) hydrogen bonds : bond 0.03138 / 2.13 ( 625) hydrogen bonds : angle 5.35939 / 3.83 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.6395 (mt0) cc_final: 0.5909 (mt0) REVERT: A 116 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6391 (mmt) REVERT: A 122 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 199 SER cc_start: 0.6998 (m) cc_final: 0.6544 (t) REVERT: A 234 LYS cc_start: 0.6779 (mmpt) cc_final: 0.6197 (mtmm) REVERT: A 247 GLU cc_start: 0.6289 (mt-10) cc_final: 0.6068 (mt-10) REVERT: A 286 LYS cc_start: 0.7356 (tptp) cc_final: 0.6785 (ttpp) REVERT: A 308 TYR cc_start: 0.5952 (m-10) cc_final: 0.5735 (m-10) REVERT: A 311 LYS cc_start: 0.6087 (tptp) cc_final: 0.4817 (ptpt) REVERT: B 81 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: B 110 GLN cc_start: 0.6525 (mt0) cc_final: 0.6098 (mt0) REVERT: B 199 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6641 (t) REVERT: B 221 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6053 (mmm) REVERT: B 249 MET cc_start: 0.6720 (mtp) cc_final: 0.6102 (mtp) REVERT: B 259 MET cc_start: 0.6488 (ptp) cc_final: 0.5433 (ttp) REVERT: B 261 ASP cc_start: 0.6890 (m-30) cc_final: 0.6414 (m-30) REVERT: B 286 LYS cc_start: 0.7199 (tptp) cc_final: 0.6611 (ttpp) REVERT: B 316 MET cc_start: 0.6636 (tmm) cc_final: 0.6247 (tpp) REVERT: B 325 LEU cc_start: 0.7350 (tt) cc_final: 0.7093 (tm) REVERT: C 110 GLN cc_start: 0.6004 (mt0) cc_final: 0.5562 (mt0) REVERT: C 116 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.5774 (mmt) REVERT: C 199 SER cc_start: 0.7010 (m) cc_final: 0.6574 (t) REVERT: C 221 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6357 (mmm) REVERT: C 230 GLU cc_start: 0.7353 (tp30) cc_final: 0.6910 (tp30) REVERT: C 247 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5897 (mt-10) REVERT: C 258 MET cc_start: 0.6664 (ptt) cc_final: 0.6407 (ptt) REVERT: C 286 LYS cc_start: 0.7523 (tptp) cc_final: 0.7073 (ttpp) REVERT: C 308 TYR cc_start: 0.5979 (m-10) cc_final: 0.5736 (m-10) REVERT: D 116 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6008 (mmt) REVERT: D 122 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: D 197 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: D 199 SER cc_start: 0.7040 (m) cc_final: 0.6590 (t) REVERT: D 221 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6329 (mmm) REVERT: D 230 GLU cc_start: 0.7536 (tp30) cc_final: 0.7064 (tp30) REVERT: D 247 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5922 (mt-10) REVERT: D 258 MET cc_start: 0.6890 (ptt) cc_final: 0.6640 (ptt) outliers start: 51 outliers final: 29 residues processed: 246 average time/residue: 0.5266 time to fit residues: 143.1758 Evaluate side-chains 241 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.195462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169069 restraints weight = 14574.046| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.52 r_work: 0.3858 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13492 Z= 0.169 Angle : 0.674 10.314 18360 Z= 0.339 Chirality : 0.046 0.259 1948 Planarity : 0.006 0.079 2344 Dihedral : 5.842 59.754 1827 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.25 % Allowed : 23.80 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1632 helix: 0.74 (0.20), residues: 664 sheet: -0.51 (0.34), residues: 308 loop : -0.14 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 198 TYR 0.024 0.002 TYR C 264 PHE 0.021 0.002 PHE D 226 TRP 0.019 0.002 TRP B 317 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (13492) covalent geometry : angle 0.67432 / 0.34 (18360) hydrogen bonds : bond 0.03750 / 2.53 ( 625) hydrogen bonds : angle 5.69436 / 4.07 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.59 seconds wall clock time: 74 minutes 49.63 seconds (4489.63 seconds total)