Starting phenix.real_space_refine on Wed May 14 15:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgp_40463/05_2025/8sgp_40463.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgp_40463/05_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_40463/05_2025/8sgp_40463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgp_40463/05_2025/8sgp_40463.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgp_40463/05_2025/8sgp_40463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgp_40463/05_2025/8sgp_40463.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 7.04, per 1000 atoms: 0.58 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: 3.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.36 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: 3.77 Time building geometry restraints manager: 3.67 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP B 342 HIS 0.001 0.000 HIS D 316 PHE 0.005 0.001 PHE C 321 TYR 0.016 0.001 TYR A 337 ARG 0.002 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.13997 ( 744) hydrogen bonds : angle 5.24916 ( 2112) covalent geometry : bond 0.00376 (12340) covalent geometry : angle 0.50567 (16680) *********************** 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 : 1.366 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 180 average time/residue: 1.5818 time to fit residues: 304.4086 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 : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 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 45 GLN A 88 ASN A 120 GLN A 130 GLN A 194 ASN A 199 ASN A 261 ASN A 293 GLN A 317 GLN A 338 GLN A 398 GLN A 405 GLN B 45 GLN B 88 ASN B 120 GLN B 130 GLN B 194 ASN B 199 ASN B 261 ASN B 293 GLN B 317 GLN B 338 GLN B 398 GLN B 405 GLN C 45 GLN C 88 ASN C 120 GLN C 130 GLN C 194 ASN C 199 ASN C 261 ASN C 293 GLN C 317 GLN C 338 GLN C 398 GLN C 405 GLN D 45 GLN D 88 ASN D 120 GLN D 130 GLN D 194 ASN D 199 ASN D 261 ASN D 293 GLN D 317 GLN D 338 GLN D 398 GLN D 405 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.075984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.062685 restraints weight = 20586.986| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.29 r_work: 0.2540 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12340 Z= 0.156 Angle : 0.516 6.970 16680 Z= 0.263 Chirality : 0.041 0.163 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.364 133.337 1860 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.07 % Allowed : 10.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1532 helix: 2.53 (0.17), residues: 812 sheet: -0.62 (0.35), residues: 188 loop : 0.37 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 200 HIS 0.001 0.000 HIS B 316 PHE 0.007 0.001 PHE D 381 TYR 0.016 0.002 TYR B 352 ARG 0.002 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 744) hydrogen bonds : angle 4.15393 ( 2112) covalent geometry : bond 0.00362 (12340) covalent geometry : angle 0.51568 (16680) *********************** 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 135 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.438 Fit side-chains outliers start: 37 outliers final: 12 residues processed: 119 average time/residue: 1.3856 time to fit residues: 178.4378 Evaluate side-chains 96 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 61 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 407 GLN B 242 GLN B 407 GLN C 242 GLN C 407 GLN D 242 GLN D 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.074866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.061307 restraints weight = 21025.719| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.31 r_work: 0.2512 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12340 Z= 0.172 Angle : 0.502 6.088 16680 Z= 0.258 Chirality : 0.041 0.142 1788 Planarity : 0.003 0.029 2152 Dihedral : 10.205 128.276 1860 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.65 % Allowed : 9.39 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1532 helix: 2.49 (0.17), residues: 812 sheet: -0.84 (0.34), residues: 188 loop : 0.39 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 200 HIS 0.001 0.000 HIS C 316 PHE 0.008 0.001 PHE A 381 TYR 0.017 0.002 TYR D 352 ARG 0.002 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 744) hydrogen bonds : angle 4.01043 ( 2112) covalent geometry : bond 0.00407 (12340) covalent geometry : angle 0.50194 (16680) *********************** 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: 44 poor density : 91 time to evaluate : 1.305 Fit side-chains outliers start: 44 outliers final: 16 residues processed: 119 average time/residue: 1.3990 time to fit residues: 179.7078 Evaluate side-chains 108 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.077175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.063713 restraints weight = 20505.615| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.33 r_work: 0.2568 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12340 Z= 0.109 Angle : 0.455 5.727 16680 Z= 0.233 Chirality : 0.040 0.142 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.976 120.136 1860 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.99 % Allowed : 10.80 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.22), residues: 1532 helix: 2.47 (0.17), residues: 836 sheet: -0.93 (0.34), residues: 188 loop : 0.53 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 200 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE D 381 TYR 0.013 0.001 TYR A 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 744) hydrogen bonds : angle 3.77923 ( 2112) covalent geometry : bond 0.00241 (12340) covalent geometry : angle 0.45537 (16680) *********************** 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 136 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.265 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 128 average time/residue: 1.4182 time to fit residues: 195.6519 Evaluate side-chains 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.076729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.062915 restraints weight = 20704.704| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.34 r_work: 0.2543 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12340 Z= 0.133 Angle : 0.482 5.854 16680 Z= 0.244 Chirality : 0.040 0.136 1788 Planarity : 0.003 0.026 2152 Dihedral : 9.737 115.515 1860 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.74 % Allowed : 12.87 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1532 helix: 2.43 (0.17), residues: 836 sheet: -0.88 (0.35), residues: 188 loop : 0.53 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE D 202 TYR 0.017 0.001 TYR B 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 744) hydrogen bonds : angle 3.80468 ( 2112) covalent geometry : bond 0.00309 (12340) covalent geometry : angle 0.48232 (16680) *********************** 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 112 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.304 Fit side-chains REVERT: A 349 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8377 (ttp80) REVERT: B 263 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7810 (mm) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 1.3605 time to fit residues: 153.1218 Evaluate side-chains 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 263 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.063274 restraints weight = 20882.912| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.37 r_work: 0.2571 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12340 Z= 0.121 Angle : 0.468 5.751 16680 Z= 0.239 Chirality : 0.040 0.135 1788 Planarity : 0.003 0.026 2152 Dihedral : 9.462 109.626 1860 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.83 % Allowed : 12.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.22), residues: 1532 helix: 2.43 (0.17), residues: 836 sheet: -0.79 (0.35), residues: 188 loop : 0.54 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE D 202 TYR 0.016 0.001 TYR B 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 744) hydrogen bonds : angle 3.76121 ( 2112) covalent geometry : bond 0.00276 (12340) covalent geometry : angle 0.46804 (16680) *********************** 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 109 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.320 Fit side-chains REVERT: A 217 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8909 (mtmm) REVERT: A 349 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8382 (ttp80) REVERT: B 349 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8444 (ttp80) REVERT: C 349 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8457 (ttp80) REVERT: D 349 ARG cc_start: 0.8736 (ttp-110) cc_final: 0.8464 (ttp80) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 1.4237 time to fit residues: 159.8313 Evaluate side-chains 100 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 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 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU 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 26 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 78 optimal weight: 0.0470 chunk 115 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.077310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.063746 restraints weight = 20696.421| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.31 r_work: 0.2589 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1893 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= 0.113 Angle : 0.460 5.726 16680 Z= 0.234 Chirality : 0.040 0.133 1788 Planarity : 0.003 0.026 2152 Dihedral : 9.273 104.190 1860 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 11.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.22), residues: 1532 helix: 2.46 (0.17), residues: 836 sheet: -0.78 (0.35), residues: 188 loop : 0.55 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 191 HIS 0.001 0.000 HIS D 415 PHE 0.005 0.001 PHE D 202 TYR 0.016 0.001 TYR B 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 744) hydrogen bonds : angle 3.70500 ( 2112) covalent geometry : bond 0.00254 (12340) covalent geometry : angle 0.45998 (16680) *********************** 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 121 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.394 Fit side-chains REVERT: A 217 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8891 (mtmm) REVERT: A 263 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7755 (mm) REVERT: A 349 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8387 (ttp80) REVERT: B 217 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8894 (mtmm) REVERT: B 349 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8432 (ttp80) REVERT: C 263 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 349 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8434 (ttp80) REVERT: D 217 LYS cc_start: 0.9232 (mtpp) cc_final: 0.8886 (mtmm) REVERT: D 349 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8436 (ttp80) outliers start: 29 outliers final: 15 residues processed: 113 average time/residue: 1.3874 time to fit residues: 169.8053 Evaluate side-chains 110 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 263 LEU 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 263 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.075153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.061108 restraints weight = 20897.165| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.37 r_work: 0.2510 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12340 Z= 0.183 Angle : 0.502 6.024 16680 Z= 0.258 Chirality : 0.042 0.131 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.352 103.350 1860 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.33 % Allowed : 12.13 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.22), residues: 1532 helix: 2.45 (0.17), residues: 812 sheet: -0.74 (0.35), residues: 188 loop : 0.52 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 191 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE D 202 TYR 0.020 0.002 TYR B 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 744) hydrogen bonds : angle 3.87590 ( 2112) covalent geometry : bond 0.00436 (12340) covalent geometry : angle 0.50250 (16680) *********************** 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 118 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.488 Fit side-chains REVERT: A 217 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8896 (mtmm) REVERT: A 349 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8392 (ttp80) REVERT: B 217 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8898 (mtmm) REVERT: B 349 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8437 (ttp80) REVERT: C 217 LYS cc_start: 0.9239 (mtpp) cc_final: 0.8884 (mtmm) REVERT: C 349 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.8440 (ttp80) REVERT: D 217 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8895 (mtmm) REVERT: D 349 ARG cc_start: 0.8711 (ttp-110) cc_final: 0.8435 (ttp80) outliers start: 28 outliers final: 11 residues processed: 111 average time/residue: 1.4290 time to fit residues: 171.5377 Evaluate side-chains 102 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR 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 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU 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 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.063752 restraints weight = 20540.626| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.33 r_work: 0.2582 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1942 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= 0.108 Angle : 0.465 5.565 16680 Z= 0.238 Chirality : 0.040 0.178 1788 Planarity : 0.003 0.026 2152 Dihedral : 9.051 97.225 1860 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 12.13 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1532 helix: 2.39 (0.17), residues: 836 sheet: -0.75 (0.35), residues: 188 loop : 0.68 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 191 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE B 202 TYR 0.015 0.001 TYR B 337 ARG 0.001 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 744) hydrogen bonds : angle 3.72707 ( 2112) covalent geometry : bond 0.00235 (12340) covalent geometry : angle 0.46519 (16680) *********************** 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 108 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.264 Fit side-chains REVERT: A 349 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8413 (ttp80) REVERT: B 217 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8891 (mtmm) REVERT: B 349 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8420 (ttp80) REVERT: C 349 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8465 (ttp80) REVERT: D 349 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.8455 (ttp80) outliers start: 23 outliers final: 10 residues processed: 101 average time/residue: 1.4310 time to fit residues: 155.8427 Evaluate side-chains 92 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR 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 C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU 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 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.076884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.062923 restraints weight = 20526.051| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.35 r_work: 0.2551 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12340 Z= 0.132 Angle : 0.476 5.803 16680 Z= 0.244 Chirality : 0.041 0.180 1788 Planarity : 0.003 0.026 2152 Dihedral : 8.957 96.564 1860 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1532 helix: 2.36 (0.17), residues: 836 sheet: -0.74 (0.35), residues: 188 loop : 0.69 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.001 0.000 HIS C 415 PHE 0.006 0.001 PHE D 202 TYR 0.017 0.001 TYR D 337 ARG 0.001 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 744) hydrogen bonds : angle 3.76073 ( 2112) covalent geometry : bond 0.00307 (12340) covalent geometry : angle 0.47640 (16680) ********************** 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: 19 poor density : 85 time to evaluate : 1.408 Fit side-chains REVERT: A 349 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8414 (ttp80) REVERT: B 349 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8420 (ttp80) REVERT: C 349 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8446 (ttp80) REVERT: D 349 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8441 (ttp80) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 1.4212 time to fit residues: 155.3454 Evaluate side-chains 95 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR 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 133 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU 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 337 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.077899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.064336 restraints weight = 20516.983| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.32 r_work: 0.2592 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1993 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= 0.109 Angle : 0.464 6.402 16680 Z= 0.236 Chirality : 0.040 0.172 1788 Planarity : 0.003 0.026 2152 Dihedral : 8.773 92.491 1860 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 12.71 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.22), residues: 1532 helix: 2.40 (0.17), residues: 836 sheet: -0.77 (0.35), residues: 188 loop : 0.73 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 191 HIS 0.001 0.000 HIS C 415 PHE 0.005 0.001 PHE D 202 TYR 0.015 0.001 TYR C 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 744) hydrogen bonds : angle 3.68606 ( 2112) covalent geometry : bond 0.00242 (12340) covalent geometry : angle 0.46402 (16680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6699.70 seconds wall clock time: 116 minutes 45.84 seconds (7005.84 seconds total)