Starting phenix.real_space_refine on Sat Nov 16 20:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_40463.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_40463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_40463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_40463.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgp_40463/11_2024/8sgp_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-5513/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: 6.37, per 1000 atoms: 0.53 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 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: 1.14 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: 4.20 Time building geometry restraints manager: 3.33 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- 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= 0.229 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 *********************** 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 : 1.367 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 180 average time/residue: 1.6758 time to fit residues: 321.8464 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 : 1.423 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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= 0.233 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 *********************** 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 : 1.069 Fit side-chains outliers start: 37 outliers final: 12 residues processed: 119 average time/residue: 1.5340 time to fit residues: 196.6436 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 : 1.499 ------------------------------------------------------------------------------- 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 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 242 GLN D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12340 Z= 0.383 Angle : 0.555 6.570 16680 Z= 0.287 Chirality : 0.044 0.135 1788 Planarity : 0.004 0.031 2152 Dihedral : 10.217 127.412 1860 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.99 % Allowed : 9.39 % Favored : 86.63 % 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: 1.84 (0.21), residues: 1532 helix: 2.36 (0.17), residues: 812 sheet: -0.84 (0.34), residues: 188 loop : 0.30 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 200 HIS 0.002 0.001 HIS C 316 PHE 0.012 0.001 PHE A 381 TYR 0.021 0.002 TYR B 352 ARG 0.003 0.000 ARG B 53 *********************** 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 139 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 1.516 Fit side-chains outliers start: 48 outliers final: 19 residues processed: 123 average time/residue: 1.5992 time to fit residues: 211.7168 Evaluate side-chains 108 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 337 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.169 Angle : 0.468 5.649 16680 Z= 0.241 Chirality : 0.040 0.144 1788 Planarity : 0.003 0.028 2152 Dihedral : 10.074 119.225 1860 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.74 % Allowed : 11.71 % Favored : 86.54 % 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: 1.97 (0.22), residues: 1532 helix: 2.48 (0.17), residues: 816 sheet: -0.93 (0.34), residues: 188 loop : 0.38 (0.28), residues: 528 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 A 381 TYR 0.013 0.001 TYR A 337 ARG 0.001 0.000 ARG A 80 *********************** 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 114 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.335 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 106 average time/residue: 1.4550 time to fit residues: 166.6868 Evaluate side-chains 96 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.0000 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12340 Z= 0.249 Angle : 0.491 6.012 16680 Z= 0.252 Chirality : 0.041 0.134 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.867 115.491 1860 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.99 % Allowed : 12.13 % Favored : 85.88 % 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: 1.94 (0.21), residues: 1532 helix: 2.47 (0.17), residues: 812 sheet: -0.87 (0.34), residues: 188 loop : 0.34 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 191 HIS 0.001 0.000 HIS C 316 PHE 0.007 0.001 PHE C 381 TYR 0.018 0.002 TYR C 337 ARG 0.001 0.000 ARG A 53 *********************** 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 117 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.322 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 106 average time/residue: 1.6161 time to fit residues: 183.8619 Evaluate side-chains 99 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1851 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= 0.202 Angle : 0.489 5.794 16680 Z= 0.248 Chirality : 0.040 0.133 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.618 110.788 1860 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.49 % Allowed : 12.62 % Favored : 84.88 % 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 (0.22), residues: 1532 helix: 2.49 (0.18), residues: 816 sheet: -0.82 (0.35), residues: 188 loop : 0.37 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 191 HIS 0.001 0.000 HIS D 415 PHE 0.006 0.001 PHE C 202 TYR 0.016 0.001 TYR C 337 ARG 0.001 0.000 ARG A 53 *********************** 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 118 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.379 Fit side-chains outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 1.6179 time to fit residues: 182.9221 Evaluate side-chains 101 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1898 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= 0.193 Angle : 0.476 5.787 16680 Z= 0.244 Chirality : 0.040 0.136 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.403 105.572 1860 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.83 % Allowed : 12.79 % 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: 2.01 (0.22), residues: 1532 helix: 2.42 (0.17), residues: 836 sheet: -0.80 (0.35), residues: 188 loop : 0.44 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.001 0.000 HIS D 316 PHE 0.006 0.001 PHE D 202 TYR 0.016 0.001 TYR B 337 ARG 0.001 0.000 ARG D 53 *********************** 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 101 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.373 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 93 average time/residue: 1.5315 time to fit residues: 153.6937 Evaluate side-chains 93 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12340 Z= 0.317 Angle : 0.522 6.090 16680 Z= 0.269 Chirality : 0.042 0.132 1788 Planarity : 0.003 0.029 2152 Dihedral : 9.466 104.739 1860 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 12.38 % 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: 1.89 (0.21), residues: 1532 helix: 2.36 (0.17), residues: 816 sheet: -0.75 (0.35), residues: 188 loop : 0.36 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE C 202 TYR 0.020 0.002 TYR B 337 ARG 0.002 0.000 ARG A 53 *********************** 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 108 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.457 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 100 average time/residue: 1.6461 time to fit residues: 176.9710 Evaluate side-chains 93 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.190 Angle : 0.491 5.615 16680 Z= 0.250 Chirality : 0.041 0.182 1788 Planarity : 0.003 0.028 2152 Dihedral : 9.186 99.372 1860 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 12.38 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.22), residues: 1532 helix: 2.44 (0.17), residues: 816 sheet: -0.78 (0.35), residues: 188 loop : 0.48 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 191 HIS 0.001 0.000 HIS C 316 PHE 0.007 0.001 PHE B 202 TYR 0.016 0.002 TYR B 337 ARG 0.001 0.000 ARG A 53 *********************** 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 104 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.413 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 96 average time/residue: 1.7329 time to fit residues: 179.1982 Evaluate side-chains 96 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12340 Z= 0.144 Angle : 0.456 5.700 16680 Z= 0.232 Chirality : 0.040 0.170 1788 Planarity : 0.003 0.027 2152 Dihedral : 8.795 92.665 1860 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.83 % Allowed : 12.13 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1532 helix: 2.46 (0.17), residues: 836 sheet: -0.77 (0.35), residues: 188 loop : 0.63 (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 0.005 0.001 PHE D 202 TYR 0.014 0.001 TYR B 337 ARG 0.001 0.000 ARG A 53 ********************** 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 111 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.460 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 1.5900 time to fit residues: 176.1703 Evaluate side-chains 97 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.0030 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.0570 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- 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 = 0.2998 r_free = 0.2998 target = 0.079150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065799 restraints weight = 20424.543| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.30 r_work: 0.2628 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12340 Z= 0.127 Angle : 0.450 5.665 16680 Z= 0.228 Chirality : 0.039 0.165 1788 Planarity : 0.003 0.026 2152 Dihedral : 8.549 88.244 1860 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 2.22 (0.22), residues: 1532 helix: 2.47 (0.17), residues: 840 sheet: -0.68 (0.35), residues: 188 loop : 0.75 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 200 HIS 0.002 0.000 HIS D 90 PHE 0.004 0.001 PHE B 381 TYR 0.015 0.001 TYR A 337 ARG 0.001 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.05 seconds wall clock time: 69 minutes 57.02 seconds (4197.02 seconds total)