Starting phenix.real_space_refine on Sat Aug 23 12:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgp_40463/08_2025/8sgp_40463.cif" } resolution = 2.69 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= 0.002 sd= 0.020 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 72 5.16 5 C 7632 2.51 5 N 2080 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2972 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.74, per 1000 atoms: 0.14 Number of scatterers: 12100 At special positions: 0 Unit cell: (96.5835, 93.2815, 98.2345, 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 72 16.00 P 8 15.00 O 2308 8.00 N 2080 7.00 C 7632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 419.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 62.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 42 through 71 removed outlier: 5.267A pdb=" N ILE A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 4.467A pdb=" N ALA A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 116 through 136 removed outlier: 4.119A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 138 through 152 removed outlier: 4.133A pdb=" N ARG A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 268 through 304 removed outlier: 3.510A pdb=" N VAL A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 316 through 346 Processing helix chain 'A' and resid 350 through 377 removed outlier: 3.551A pdb=" N ASN A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.560A pdb=" N PHE A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'B' and resid 42 through 71 removed outlier: 5.267A pdb=" N ILE B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix removed outlier: 4.468A pdb=" N ALA B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 116 through 136 removed outlier: 4.119A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 138 through 152 removed outlier: 4.132A pdb=" N ARG B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET B 149 " --> pdb=" O TYR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 268 through 304 removed outlier: 3.510A pdb=" N VAL B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Proline residue: B 282 - end of helix Processing helix chain 'B' and resid 316 through 346 Processing helix chain 'B' and resid 350 through 377 removed outlier: 3.551A pdb=" N ASN B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 377 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.561A pdb=" N PHE B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'C' and resid 42 through 71 removed outlier: 5.268A pdb=" N ILE C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 4.467A pdb=" N ALA C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 101 through 116 Processing helix chain 'C' and resid 116 through 136 removed outlier: 4.119A pdb=" N ASN C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Proline residue: C 132 - end of helix Processing helix chain 'C' and resid 138 through 152 removed outlier: 4.133A pdb=" N ARG C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET C 149 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 214 through 217 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 268 through 304 removed outlier: 3.509A pdb=" N VAL C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Proline residue: C 282 - end of helix Processing helix chain 'C' and resid 316 through 346 Processing helix chain 'C' and resid 350 through 377 removed outlier: 3.551A pdb=" N ASN C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 377 " --> pdb=" O VAL C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.560A pdb=" N PHE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'D' and resid 42 through 71 removed outlier: 5.267A pdb=" N ILE D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Proline residue: D 62 - end of helix removed outlier: 4.467A pdb=" N ALA D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU D 66 " --> pdb=" O PRO D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 101 through 116 Processing helix chain 'D' and resid 116 through 136 removed outlier: 4.118A pdb=" N ASN D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Proline residue: D 132 - end of helix Processing helix chain 'D' and resid 138 through 152 removed outlier: 4.132A pdb=" N ARG D 148 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET D 149 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 214 through 217 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 268 through 304 removed outlier: 3.509A pdb=" N VAL D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 316 through 346 Processing helix chain 'D' and resid 350 through 377 removed outlier: 3.550A pdb=" N ASN D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 377 " --> pdb=" O VAL D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.561A pdb=" N PHE D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 403 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.277A pdb=" N TYR A 183 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 256 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE A 185 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 191 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 248 " --> pdb=" O TRP A 191 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 247 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS A 236 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY A 249 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AA5, first strand: chain 'B' and resid 175 through 179 removed outlier: 6.277A pdb=" N TYR B 183 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS B 256 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE B 185 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP B 191 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG B 248 " --> pdb=" O TRP B 191 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR B 247 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS B 236 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY B 249 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 179 removed outlier: 6.277A pdb=" N TYR C 183 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS C 256 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE C 185 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 191 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG C 248 " --> pdb=" O TRP C 191 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR C 247 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS C 236 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY C 249 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AB2, first strand: chain 'D' and resid 175 through 179 removed outlier: 6.277A pdb=" N TYR D 183 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS D 256 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE D 185 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP D 191 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG D 248 " --> pdb=" O TRP D 191 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR D 247 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS D 236 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY D 249 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 307 through 308 744 hydrogen bonds defined for protein. 2112 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: 1.72 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4011 1.34 - 1.46: 2522 1.46 - 1.58: 5679 1.58 - 1.69: 8 1.69 - 1.81: 120 Bond restraints: 12340 Sorted by residual: bond pdb=" O3P FAD D 501 " pdb=" P FAD D 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O5B FAD C 501 " pdb=" PA FAD C 501 " ideal model delta sigma weight residual 1.634 1.569 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 12335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 16426 1.43 - 2.86: 163 2.86 - 4.29: 51 4.29 - 5.72: 20 5.72 - 7.15: 20 Bond angle restraints: 16680 Sorted by residual: angle pdb=" O1P FAD D 501 " pdb=" P FAD D 501 " pdb=" O2P FAD D 501 " ideal model delta sigma weight residual 122.50 115.35 7.15 3.00e+00 1.11e-01 5.68e+00 angle pdb=" O1P FAD C 501 " pdb=" P FAD C 501 " pdb=" O2P FAD C 501 " ideal model delta sigma weight residual 122.50 115.35 7.15 3.00e+00 1.11e-01 5.68e+00 angle pdb=" O1P FAD B 501 " pdb=" P FAD B 501 " pdb=" O2P FAD B 501 " ideal model delta sigma weight residual 122.50 115.36 7.14 3.00e+00 1.11e-01 5.66e+00 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 115.38 7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" P FAD B 501 " pdb=" O3P FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 130.34 123.88 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 16675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 7301 27.08 - 54.16: 143 54.16 - 81.24: 32 81.24 - 108.32: 0 108.32 - 135.40: 4 Dihedral angle restraints: 7480 sinusoidal: 3108 harmonic: 4372 Sorted by residual: dihedral pdb=" O5' FAD C 501 " pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " pdb=" PA FAD C 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.83 135.40 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O5' FAD A 501 " pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.85 135.38 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O5' FAD B 501 " pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sinusoidal sigma weight residual 298.23 162.85 135.38 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 7477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1217 0.033 - 0.066: 402 0.066 - 0.100: 120 0.100 - 0.133: 45 0.133 - 0.166: 4 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C2B FAD D 501 " pdb=" C1B FAD D 501 " pdb=" C3B FAD D 501 " pdb=" O2B FAD D 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1785 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 281 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO D 282 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 282 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 281 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 282 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 281 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO C 282 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 282 " -0.016 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 376 2.72 - 3.26: 12098 3.26 - 3.81: 20307 3.81 - 4.35: 26252 4.35 - 4.90: 44238 Nonbonded interactions: 103271 Sorted by model distance: nonbonded pdb=" OH TYR A 419 " pdb=" OD1 ASP D 297 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR B 419 " pdb=" OD1 ASP C 297 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASP B 297 " pdb=" OH TYR C 419 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 297 " pdb=" OH TYR D 419 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU D 110 " pdb=" OH TYR D 337 " model vdw 2.186 3.040 ... (remaining 103266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.079 12340 Z= 0.190 Angle : 0.506 7.151 16680 Z= 0.239 Chirality : 0.040 0.166 1788 Planarity : 0.003 0.028 2152 Dihedral : 11.583 135.399 4704 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.33 % Allowed : 6.64 % Favored : 92.03 % 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 aren not related in a simple way. whole: 2.13 (0.21), residues: 1532 helix: 2.50 (0.17), residues: 812 sheet: 0.09 (0.38), residues: 180 loop : 0.27 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 53 TYR 0.016 0.001 TYR A 337 PHE 0.005 0.001 PHE C 321 TRP 0.002 0.000 TRP B 342 HIS 0.001 0.000 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00376 (12340) covalent geometry : angle 0.50567 (16680) hydrogen bonds : bond 0.13997 ( 744) hydrogen bonds : angle 5.24916 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.304 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 180 average time/residue: 0.6728 time to fit residues: 129.1028 Evaluate side-chains 92 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 199 ASN A 261 ASN A 293 GLN A 317 GLN A 338 GLN A 398 GLN A 405 GLN A 407 GLN B 45 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 199 ASN B 261 ASN B 293 GLN B 317 GLN B 338 GLN B 398 GLN B 405 GLN B 407 GLN C 45 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 199 ASN C 261 ASN C 293 GLN C 317 GLN C 338 GLN C 398 GLN C 405 GLN C 407 GLN D 45 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 199 ASN D 261 ASN D 293 GLN D 317 GLN D 338 GLN D 398 GLN D 405 GLN D 407 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.077811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.064595 restraints weight = 20646.161| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.31 r_work: 0.2586 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.117 Angle : 0.493 6.699 16680 Z= 0.250 Chirality : 0.040 0.165 1788 Planarity : 0.003 0.027 2152 Dihedral : 10.387 133.912 1860 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.74 % Allowed : 10.55 % Favored : 86.71 % 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 aren not related in a simple way. whole: 2.10 (0.22), residues: 1532 helix: 2.48 (0.17), residues: 836 sheet: -0.63 (0.35), residues: 188 loop : 0.46 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 53 TYR 0.014 0.001 TYR C 352 PHE 0.005 0.001 PHE C 202 TRP 0.007 0.001 TRP C 200 HIS 0.001 0.000 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00256 (12340) covalent geometry : angle 0.49332 (16680) hydrogen bonds : bond 0.04329 ( 744) hydrogen bonds : angle 4.05908 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.404 Fit side-chains outliers start: 33 outliers final: 12 residues processed: 112 average time/residue: 0.6158 time to fit residues: 74.2879 Evaluate side-chains 94 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.075789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.062206 restraints weight = 21004.902| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.34 r_work: 0.2530 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12340 Z= 0.152 Angle : 0.488 6.031 16680 Z= 0.250 Chirality : 0.041 0.139 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.208 128.780 1860 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.32 % Allowed : 9.97 % Favored : 86.71 % 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 aren not related in a simple way. whole: 2.07 (0.21), residues: 1532 helix: 2.54 (0.17), residues: 812 sheet: -0.80 (0.35), residues: 188 loop : 0.46 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.017 0.002 TYR D 352 PHE 0.008 0.001 PHE C 381 TRP 0.006 0.001 TRP D 200 HIS 0.001 0.000 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00356 (12340) covalent geometry : angle 0.48850 (16680) hydrogen bonds : bond 0.04617 ( 744) hydrogen bonds : angle 3.95626 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.325 Fit side-chains outliers start: 40 outliers final: 16 residues processed: 121 average time/residue: 0.5668 time to fit residues: 74.1495 Evaluate side-chains 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** 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 = 0.2966 r_free = 0.2966 target = 0.077459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063981 restraints weight = 20796.054| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.33 r_work: 0.2572 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12340 Z= 0.110 Angle : 0.458 5.735 16680 Z= 0.233 Chirality : 0.040 0.140 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.986 121.155 1860 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.16 % Allowed : 10.80 % Favored : 87.04 % 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 aren not related in a simple way. whole: 2.09 (0.22), residues: 1532 helix: 2.47 (0.17), residues: 836 sheet: -0.86 (0.34), residues: 188 loop : 0.56 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.014 0.001 TYR D 337 PHE 0.006 0.001 PHE C 381 TRP 0.005 0.001 TRP C 200 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00244 (12340) covalent geometry : angle 0.45778 (16680) hydrogen bonds : bond 0.04082 ( 744) hydrogen bonds : angle 3.77463 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.475 Fit side-chains outliers start: 26 outliers final: 8 residues processed: 117 average time/residue: 0.6152 time to fit residues: 77.4827 Evaluate side-chains 103 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 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 = 0.2950 r_free = 0.2950 target = 0.076575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.062751 restraints weight = 20796.507| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.36 r_work: 0.2544 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12340 Z= 0.140 Angle : 0.483 5.882 16680 Z= 0.245 Chirality : 0.040 0.135 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.775 116.582 1860 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.74 % Allowed : 11.96 % Favored : 86.30 % 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 aren not related in a simple way. whole: 2.07 (0.22), residues: 1532 helix: 2.44 (0.17), residues: 836 sheet: -0.83 (0.35), residues: 188 loop : 0.54 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 53 TYR 0.018 0.002 TYR B 337 PHE 0.007 0.001 PHE B 381 TRP 0.006 0.001 TRP C 191 HIS 0.001 0.000 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00327 (12340) covalent geometry : angle 0.48265 (16680) hydrogen bonds : bond 0.04386 ( 744) hydrogen bonds : angle 3.80394 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.387 Fit side-chains REVERT: A 349 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8372 (ttp80) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.6450 time to fit residues: 71.5925 Evaluate side-chains 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** 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 = 0.2911 r_free = 0.2911 target = 0.074323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.060456 restraints weight = 20849.319| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.34 r_work: 0.2493 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12340 Z= 0.203 Angle : 0.522 6.091 16680 Z= 0.269 Chirality : 0.042 0.132 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.766 112.587 1860 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.16 % Allowed : 11.63 % Favored : 86.21 % 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 aren not related in a simple way. whole: 1.92 (0.21), residues: 1532 helix: 2.40 (0.17), residues: 812 sheet: -0.77 (0.35), residues: 188 loop : 0.37 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.021 0.002 TYR C 337 PHE 0.009 0.001 PHE B 381 TRP 0.007 0.001 TRP C 191 HIS 0.001 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00486 (12340) covalent geometry : angle 0.52238 (16680) hydrogen bonds : bond 0.05042 ( 744) hydrogen bonds : angle 3.96229 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.473 Fit side-chains REVERT: A 217 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8871 (mtmm) REVERT: A 349 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8404 (ttp80) REVERT: B 349 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8450 (ttp80) REVERT: C 349 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8451 (ttp80) REVERT: D 349 ARG cc_start: 0.8737 (ttp-110) cc_final: 0.8459 (ttp80) outliers start: 26 outliers final: 20 residues processed: 108 average time/residue: 0.7351 time to fit residues: 85.2893 Evaluate side-chains 107 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 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 = 0.2951 r_free = 0.2951 target = 0.076591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.062661 restraints weight = 20687.366| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.36 r_work: 0.2539 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.121 Angle : 0.471 5.622 16680 Z= 0.241 Chirality : 0.040 0.134 1788 Planarity : 0.003 0.029 2152 Dihedral : 9.423 105.708 1860 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 12.38 % Favored : 85.71 % 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 aren not related in a simple way. whole: 2.02 (0.22), residues: 1532 helix: 2.52 (0.17), residues: 812 sheet: -0.79 (0.35), residues: 188 loop : 0.39 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 53 TYR 0.016 0.001 TYR B 337 PHE 0.006 0.001 PHE D 202 TRP 0.005 0.001 TRP D 200 HIS 0.001 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00276 (12340) covalent geometry : angle 0.47054 (16680) hydrogen bonds : bond 0.04283 ( 744) hydrogen bonds : angle 3.78386 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.502 Fit side-chains REVERT: A 217 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8855 (mtmm) REVERT: A 349 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8422 (ttp80) REVERT: B 349 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8436 (ttp80) REVERT: C 349 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8461 (ttp80) REVERT: D 349 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8470 (ttp80) outliers start: 23 outliers final: 10 residues processed: 104 average time/residue: 0.7453 time to fit residues: 83.6052 Evaluate side-chains 99 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 5.9990 chunk 131 optimal weight: 0.0060 chunk 43 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 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 = 0.2989 r_free = 0.2989 target = 0.078571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.064703 restraints weight = 20691.904| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.37 r_work: 0.2605 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12340 Z= 0.097 Angle : 0.447 5.698 16680 Z= 0.227 Chirality : 0.039 0.135 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.094 98.825 1860 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.16 % Allowed : 12.38 % Favored : 85.47 % 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 aren not related in a simple way. whole: 2.16 (0.22), residues: 1532 helix: 2.48 (0.17), residues: 840 sheet: -0.76 (0.35), residues: 188 loop : 0.65 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 243 TYR 0.015 0.001 TYR C 337 PHE 0.004 0.001 PHE C 202 TRP 0.005 0.001 TRP C 200 HIS 0.001 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00207 (12340) covalent geometry : angle 0.44665 (16680) hydrogen bonds : bond 0.03788 ( 744) hydrogen bonds : angle 3.63453 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.475 Fit side-chains REVERT: A 217 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8884 (mtmm) REVERT: A 349 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8416 (ttp80) REVERT: B 349 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8424 (ttp80) REVERT: C 349 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8455 (ttp80) REVERT: D 349 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8450 (ttp80) outliers start: 26 outliers final: 10 residues processed: 115 average time/residue: 0.6444 time to fit residues: 80.5160 Evaluate side-chains 106 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.0070 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** 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 = 0.2985 r_free = 0.2985 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.064733 restraints weight = 20465.367| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.33 r_work: 0.2606 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12340 Z= 0.099 Angle : 0.452 5.708 16680 Z= 0.229 Chirality : 0.039 0.133 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.897 95.800 1860 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.99 % Allowed : 12.79 % Favored : 85.22 % 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 aren not related in a simple way. whole: 2.19 (0.22), residues: 1532 helix: 2.47 (0.17), residues: 840 sheet: -0.70 (0.35), residues: 188 loop : 0.72 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.016 0.001 TYR B 337 PHE 0.004 0.001 PHE A 202 TRP 0.005 0.001 TRP B 200 HIS 0.001 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00213 (12340) covalent geometry : angle 0.45244 (16680) hydrogen bonds : bond 0.03822 ( 744) hydrogen bonds : angle 3.61989 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.533 Fit side-chains REVERT: A 349 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8417 (ttp80) REVERT: B 349 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8421 (ttp80) REVERT: C 349 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8451 (ttp80) REVERT: D 349 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8437 (ttp80) outliers start: 24 outliers final: 10 residues processed: 112 average time/residue: 0.6870 time to fit residues: 83.4714 Evaluate side-chains 102 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** 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 = 0.2977 r_free = 0.2977 target = 0.077868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.064214 restraints weight = 20646.720| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.32 r_work: 0.2594 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.117 Angle : 0.470 5.711 16680 Z= 0.239 Chirality : 0.040 0.177 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.817 94.420 1860 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 13.46 % Favored : 85.05 % 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 aren not related in a simple way. whole: 2.22 (0.22), residues: 1532 helix: 2.44 (0.17), residues: 836 sheet: -0.39 (0.36), residues: 180 loop : 0.68 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.016 0.001 TYR D 337 PHE 0.006 0.001 PHE C 202 TRP 0.005 0.001 TRP B 191 HIS 0.001 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00266 (12340) covalent geometry : angle 0.46986 (16680) hydrogen bonds : bond 0.04048 ( 744) hydrogen bonds : angle 3.67333 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.543 Fit side-chains REVERT: A 349 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8422 (ttp80) REVERT: B 349 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8426 (ttp80) REVERT: C 349 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8440 (ttp80) REVERT: D 349 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8424 (ttp80) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.7573 time to fit residues: 81.6630 Evaluate side-chains 99 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 41 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** 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 = 0.2998 r_free = 0.2998 target = 0.079073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.065422 restraints weight = 20565.825| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.33 r_work: 0.2617 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12340 Z= 0.101 Angle : 0.461 5.667 16680 Z= 0.233 Chirality : 0.040 0.173 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.648 90.338 1860 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.41 % Allowed : 13.54 % Favored : 85.05 % 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 aren not related in a simple way. whole: 2.22 (0.22), residues: 1532 helix: 2.43 (0.17), residues: 840 sheet: -0.39 (0.36), residues: 180 loop : 0.69 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 53 TYR 0.016 0.001 TYR B 337 PHE 0.004 0.001 PHE B 202 TRP 0.005 0.001 TRP B 191 HIS 0.001 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00221 (12340) covalent geometry : angle 0.46109 (16680) hydrogen bonds : bond 0.03847 ( 744) hydrogen bonds : angle 3.63757 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.53 seconds wall clock time: 59 minutes 38.82 seconds (3578.82 seconds total)