Starting phenix.real_space_refine on Wed Jul 30 03:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgp_40463/07_2025/8sgp_40463.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgp_40463/07_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_40463/07_2025/8sgp_40463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgp_40463/07_2025/8sgp_40463.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgp_40463/07_2025/8sgp_40463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgp_40463/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.43, per 1000 atoms: 0.61 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: 2.88 Conformation dependent library (CDL) restraints added in 1.7 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: 1.62 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: 3.40 Time building geometry restraints manager: 3.45 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: 0.10 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: 2.920 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.840 Find NCS groups from input model: 0.280 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:14.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.280 ------------------------------------------------------------------------------- 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 : 1.415 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 180 average time/residue: 1.6623 time to fit residues: 318.8880 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 : 1.400 ------------------------------------------------------------------------------- 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 = 0.075983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.062660 restraints weight = 20586.892| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.31 r_work: 0.2540 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.42 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 6.969 16680 Z= 0.263 Chirality : 0.041 0.163 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.364 133.331 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 4.15380 ( 2112) covalent geometry : bond 0.00362 (12340) covalent geometry : angle 0.51565 (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 : 1.434 Fit side-chains outliers start: 37 outliers final: 12 residues processed: 119 average time/residue: 1.4665 time to fit residues: 188.2219 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 : 1.339 ------------------------------------------------------------------------------- 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: 0.0570 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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 = 0.2921 r_free = 0.2921 target = 0.075045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.061446 restraints weight = 21010.748| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.33 r_work: 0.2515 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1592 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= 0.165 Angle : 0.498 6.034 16680 Z= 0.256 Chirality : 0.041 0.142 1788 Planarity : 0.003 0.029 2152 Dihedral : 10.201 127.876 1860 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.28 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: 2.00 (0.21), residues: 1532 helix: 2.50 (0.17), residues: 812 sheet: -0.85 (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 0.009 0.001 PHE D 381 TYR 0.017 0.002 TYR B 337 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 744) hydrogen bonds : angle 3.98718 ( 2112) covalent geometry : bond 0.00390 (12340) covalent geometry : angle 0.49799 (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 : 1.428 Fit side-chains outliers start: 44 outliers final: 16 residues processed: 119 average time/residue: 1.4883 time to fit residues: 190.9093 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 : 1.364 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.2965 r_free = 0.2965 target = 0.077475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.063738 restraints weight = 20443.911| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.33 r_work: 0.2565 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1720 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 : 0.457 5.722 16680 Z= 0.235 Chirality : 0.040 0.141 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.936 119.393 1860 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.99 % Allowed : 10.96 % 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 (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: 2.05 (0.22), residues: 1532 helix: 2.45 (0.17), residues: 836 sheet: -0.93 (0.34), residues: 188 loop : 0.54 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 200 HIS 0.001 0.000 HIS D 415 PHE 0.005 0.001 PHE B 381 TYR 0.013 0.001 TYR D 337 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 744) hydrogen bonds : angle 3.80517 ( 2112) covalent geometry : bond 0.00251 (12340) covalent geometry : angle 0.45747 (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 132 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.493 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 124 average time/residue: 1.4844 time to fit residues: 198.3004 Evaluate side-chains 98 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.2948 r_free = 0.2948 target = 0.076381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.062556 restraints weight = 20714.787| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.34 r_work: 0.2536 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12340 Z= 0.142 Angle : 0.488 5.839 16680 Z= 0.247 Chirality : 0.040 0.135 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.758 115.579 1860 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.99 % Allowed : 12.54 % 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 (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: 2.41 (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 C 415 PHE 0.007 0.001 PHE C 202 TYR 0.017 0.002 TYR D 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 744) hydrogen bonds : angle 3.83202 ( 2112) covalent geometry : bond 0.00332 (12340) covalent geometry : angle 0.48772 (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 110 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.319 Fit side-chains REVERT: A 217 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8909 (mtmm) REVERT: A 349 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8379 (ttp80) outliers start: 24 outliers final: 16 residues processed: 101 average time/residue: 1.4424 time to fit residues: 157.6084 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 : 1.417 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.2971 r_free = 0.2971 target = 0.077733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.063869 restraints weight = 20857.696| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.37 r_work: 0.2584 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12340 Z= 0.109 Angle : 0.462 5.692 16680 Z= 0.234 Chirality : 0.039 0.135 1788 Planarity : 0.003 0.026 2152 Dihedral : 9.421 109.057 1860 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 12.54 % 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: 2.12 (0.22), residues: 1532 helix: 2.48 (0.17), residues: 836 sheet: -0.79 (0.35), residues: 188 loop : 0.58 (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 D 337 ARG 0.001 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 744) hydrogen bonds : angle 3.72629 ( 2112) covalent geometry : bond 0.00243 (12340) covalent geometry : angle 0.46158 (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 113 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.525 Fit side-chains REVERT: A 217 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8898 (mtmm) REVERT: A 349 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8377 (ttp80) REVERT: B 263 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 349 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8452 (ttp80) REVERT: C 349 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8452 (ttp80) REVERT: D 349 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8450 (ttp80) outliers start: 21 outliers final: 12 residues processed: 105 average time/residue: 1.4627 time to fit residues: 166.6637 Evaluate side-chains 105 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 263 LEU 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: 2.9990 chunk 149 optimal weight: 0.9990 chunk 78 optimal weight: 0.0070 chunk 115 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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 = 0.2956 r_free = 0.2956 target = 0.076808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.062925 restraints weight = 20731.980| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.35 r_work: 0.2548 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12340 Z= 0.131 Angle : 0.472 5.793 16680 Z= 0.241 Chirality : 0.040 0.133 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.334 105.557 1860 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 11.54 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.45 (0.17), residues: 836 sheet: -0.78 (0.35), residues: 188 loop : 0.57 (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 0.007 0.001 PHE B 202 TYR 0.017 0.001 TYR D 337 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 744) hydrogen bonds : angle 3.75578 ( 2112) covalent geometry : bond 0.00304 (12340) covalent geometry : angle 0.47192 (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: 32 poor density : 89 time to evaluate : 1.322 Fit side-chains REVERT: A 217 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8891 (mtmm) REVERT: A 349 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8389 (ttp80) REVERT: B 217 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8887 (mtmm) REVERT: B 263 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7831 (mm) REVERT: B 349 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8451 (ttp80) REVERT: C 263 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7828 (mm) REVERT: C 349 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8456 (ttp80) REVERT: D 217 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8886 (mtmm) REVERT: D 263 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7768 (mm) REVERT: D 349 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8438 (ttp80) outliers start: 32 outliers final: 16 residues processed: 113 average time/residue: 1.4419 time to fit residues: 175.8687 Evaluate side-chains 109 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 263 LEU 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: 0.7980 chunk 38 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 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: 1.4584 ------------------------------------------------------------------------------- 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 = 0.2922 r_free = 0.2922 target = 0.074930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.061215 restraints weight = 20912.007| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.32 r_work: 0.2513 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12340 Z= 0.176 Angle : 0.497 5.982 16680 Z= 0.256 Chirality : 0.041 0.131 1788 Planarity : 0.003 0.027 2152 Dihedral : 9.363 103.380 1860 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.57 % Allowed : 11.63 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.22), residues: 1532 helix: 2.47 (0.17), residues: 812 sheet: -0.74 (0.35), residues: 188 loop : 0.51 (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 D 316 PHE 0.008 0.001 PHE C 202 TYR 0.019 0.002 TYR D 337 ARG 0.001 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 744) hydrogen bonds : angle 3.86906 ( 2112) covalent geometry : bond 0.00417 (12340) covalent geometry : angle 0.49750 (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 119 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 1.438 Fit side-chains REVERT: A 217 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8915 (mtmm) REVERT: A 305 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: A 349 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8397 (ttp80) REVERT: B 217 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8912 (mtmm) REVERT: B 305 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8576 (pp20) REVERT: B 349 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8428 (ttp80) REVERT: C 217 LYS cc_start: 0.9240 (mtpp) cc_final: 0.8885 (mtmm) REVERT: C 349 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8451 (ttp80) REVERT: D 217 LYS cc_start: 0.9248 (mtpp) cc_final: 0.8904 (mtmm) REVERT: D 305 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8566 (pp20) REVERT: D 349 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8431 (ttp80) outliers start: 31 outliers final: 12 residues processed: 111 average time/residue: 1.3929 time to fit residues: 167.4780 Evaluate side-chains 108 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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 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 305 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: 0.5980 chunk 140 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.2953 r_free = 0.2953 target = 0.076737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.062855 restraints weight = 20563.296| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.34 r_work: 0.2543 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1920 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= 0.125 Angle : 0.478 5.643 16680 Z= 0.245 Chirality : 0.041 0.176 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.133 98.868 1860 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 12.46 % 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: 2.05 (0.22), residues: 1532 helix: 2.37 (0.17), residues: 836 sheet: -0.76 (0.35), residues: 188 loop : 0.63 (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 D 415 PHE 0.007 0.001 PHE B 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 0.04321 ( 744) hydrogen bonds : angle 3.78587 ( 2112) covalent geometry : bond 0.00284 (12340) covalent geometry : angle 0.47797 (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 114 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.524 Fit side-chains REVERT: A 349 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8411 (ttp80) REVERT: B 349 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.8438 (ttp80) REVERT: C 349 ARG cc_start: 0.8719 (ttp-110) cc_final: 0.8461 (ttp80) REVERT: D 217 LYS cc_start: 0.9239 (mtpp) cc_final: 0.8890 (mtmm) REVERT: D 349 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8454 (ttp80) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 1.4539 time to fit residues: 168.0718 Evaluate side-chains 97 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 111 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.2972 r_free = 0.2972 target = 0.077824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.063965 restraints weight = 20485.631| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.34 r_work: 0.2571 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: 0.8694 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12340 Z= 0.108 Angle : 0.476 6.385 16680 Z= 0.240 Chirality : 0.040 0.175 1788 Planarity : 0.003 0.028 2152 Dihedral : 8.909 95.114 1860 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.83 % Allowed : 12.87 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.17), residues: 836 sheet: -0.77 (0.35), residues: 188 loop : 0.67 (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 B 337 ARG 0.001 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 744) hydrogen bonds : angle 3.70802 ( 2112) covalent geometry : bond 0.00241 (12340) covalent geometry : angle 0.47644 (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 105 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.497 Fit side-chains REVERT: A 349 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8436 (ttp80) REVERT: B 349 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8415 (ttp80) REVERT: C 349 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8448 (ttp80) REVERT: D 305 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: D 349 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8455 (ttp80) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 1.5361 time to fit residues: 160.9725 Evaluate side-chains 95 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 305 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: 0.8980 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 96 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.2979 r_free = 0.2979 target = 0.078053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.064505 restraints weight = 20538.908| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.32 r_work: 0.2595 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12340 Z= 0.110 Angle : 0.473 6.278 16680 Z= 0.238 Chirality : 0.040 0.170 1788 Planarity : 0.003 0.028 2152 Dihedral : 8.638 90.415 1860 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 12.96 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.18 (0.22), residues: 1532 helix: 2.44 (0.17), residues: 836 sheet: -0.71 (0.35), residues: 188 loop : 0.75 (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 A 415 PHE 0.005 0.001 PHE C 381 TYR 0.016 0.001 TYR C 337 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 744) hydrogen bonds : angle 3.67001 ( 2112) covalent geometry : bond 0.00248 (12340) covalent geometry : angle 0.47321 (16680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7146.76 seconds wall clock time: 123 minutes 14.51 seconds (7394.51 seconds total)