Starting phenix.real_space_refine on Fri Jun 13 16:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2r_15104/06_2025/8a2r_15104.cif" } resolution = 2.17 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= 0.000 sd= 0.007 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 Be 5 3.05 5 C 9145 2.51 5 N 2445 2.21 5 O 3265 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14990 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.99, per 1000 atoms: 0.53 Number of scatterers: 14990 At special positions: 0 Unit cell: (95.215, 88.265, 191.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 F 15 9.00 O 3265 8.00 N 2445 7.00 C 9145 6.00 Be 5 4.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 51.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.747A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.958A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.518A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.747A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.518A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.905A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.958A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.555A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.706A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.706A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.307A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.655A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.554A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.555A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.307A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.746A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.554A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.307A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.554A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.306A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 743 hydrogen bonds defined for protein. 1878 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: 5.84 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4705 1.34 - 1.46: 2936 1.46 - 1.57: 6989 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14820 Sorted by residual: bond pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 14815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 19869 2.62 - 5.24: 201 5.24 - 7.86: 20 7.86 - 10.47: 5 10.47 - 13.09: 10 Bond angle restraints: 20105 Sorted by residual: angle pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " pdb=" F3 BEF D 403 " ideal model delta sigma weight residual 119.96 106.87 13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " pdb=" F3 BEF B 403 " ideal model delta sigma weight residual 119.96 106.89 13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " pdb=" F3 BEF A 403 " ideal model delta sigma weight residual 119.96 106.90 13.06 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " pdb=" F3 BEF E 403 " ideal model delta sigma weight residual 119.96 106.91 13.05 3.00e+00 1.11e-01 1.89e+01 angle pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.93 13.03 3.00e+00 1.11e-01 1.89e+01 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 8725 31.21 - 62.42: 140 62.42 - 93.63: 35 93.63 - 124.84: 0 124.84 - 156.04: 10 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.05 -156.04 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.04 -156.04 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.98 -155.98 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1054 0.027 - 0.054: 758 0.054 - 0.081: 226 0.081 - 0.107: 154 0.107 - 0.134: 38 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.64 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 321 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 322 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 321 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 322 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 321 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO E 322 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " 0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 136 2.48 - 3.09: 10379 3.09 - 3.69: 24236 3.69 - 4.30: 39005 4.30 - 4.90: 60736 Nonbonded interactions: 134492 Sorted by model distance: nonbonded pdb="MG MG B 402 " pdb=" O HOH B 526 " model vdw 1.880 2.170 nonbonded pdb="MG MG D 402 " pdb=" F2 BEF D 403 " model vdw 1.898 2.120 nonbonded pdb="MG MG E 402 " pdb=" F2 BEF E 403 " model vdw 1.899 2.120 nonbonded pdb="MG MG B 402 " pdb=" F2 BEF B 403 " model vdw 1.899 2.120 nonbonded pdb="MG MG A 402 " pdb=" F2 BEF A 403 " model vdw 1.899 2.120 ... (remaining 134487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.830 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.017 0.900 14825 Z= 1.666 Angle : 0.674 13.092 20105 Z= 0.330 Chirality : 0.044 0.134 2230 Planarity : 0.004 0.027 2565 Dihedral : 13.665 156.045 5510 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.65 % Allowed : 3.55 % Favored : 95.81 % 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: -1.52 (0.18), residues: 1795 helix: -2.41 (0.13), residues: 790 sheet: -0.72 (0.24), residues: 335 loop : 1.17 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS E 173 PHE 0.008 0.001 PHE B 262 TYR 0.007 0.001 TYR A 143 ARG 0.003 0.001 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.22470 ( 728) hydrogen bonds : angle 7.72740 ( 1878) covalent geometry : bond 0.00485 (14820) covalent geometry : angle 0.67357 (20105) Misc. bond : bond 0.89894 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 1.877 Fit side-chains REVERT: C 113 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8335 (mmtt) REVERT: C 286 ASP cc_start: 0.7612 (m-30) cc_final: 0.7386 (m-30) REVERT: C 355 MET cc_start: 0.8157 (mtp) cc_final: 0.7772 (mtt) REVERT: B 113 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8216 (mmtt) REVERT: D 123 MET cc_start: 0.8755 (mmt) cc_final: 0.8413 (mmt) REVERT: E 227 MET cc_start: 0.8889 (mmm) cc_final: 0.8503 (mmm) REVERT: E 311 ASP cc_start: 0.7853 (m-30) cc_final: 0.7653 (m-30) outliers start: 10 outliers final: 3 residues processed: 278 average time/residue: 1.5944 time to fit residues: 480.3029 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 0.2980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 173 HIS C 246 GLN C 353 GLN C 360 GLN B 173 HIS B 360 GLN D 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093445 restraints weight = 14807.063| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.28 r_work: 0.2932 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14825 Z= 0.180 Angle : 0.641 8.213 20105 Z= 0.320 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.034 2565 Dihedral : 12.506 173.245 2058 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.39 % Favored : 98.50 % Rotamer: Outliers : 2.13 % Allowed : 7.16 % Favored : 90.71 % 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: 0.49 (0.19), residues: 1795 helix: -0.24 (0.17), residues: 790 sheet: -0.31 (0.24), residues: 345 loop : 1.87 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.011 0.001 PHE C 262 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.001 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 728) hydrogen bonds : angle 5.19824 ( 1878) covalent geometry : bond 0.00408 (14820) covalent geometry : angle 0.64146 (20105) Misc. bond : bond 0.00189 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.642 Fit side-chains REVERT: C 355 MET cc_start: 0.8787 (mtp) cc_final: 0.8370 (mtt) REVERT: A 326 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7961 (pttm) REVERT: B 100 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 125 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 224 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7748 (mp0) REVERT: D 121 GLN cc_start: 0.8742 (tt0) cc_final: 0.8414 (tm-30) REVERT: E 311 ASP cc_start: 0.8596 (m-30) cc_final: 0.8209 (m-30) outliers start: 33 outliers final: 14 residues processed: 224 average time/residue: 1.4723 time to fit residues: 358.6402 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 246 GLN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093886 restraints weight = 14750.014| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.25 r_work: 0.2947 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14825 Z= 0.147 Angle : 0.602 7.930 20105 Z= 0.295 Chirality : 0.045 0.177 2230 Planarity : 0.004 0.034 2565 Dihedral : 12.380 170.805 2058 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.83 % Rotamer: Outliers : 1.81 % Allowed : 8.06 % Favored : 90.13 % 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: 1.26 (0.20), residues: 1795 helix: 0.53 (0.19), residues: 775 sheet: -0.20 (0.24), residues: 345 loop : 2.22 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE C 262 TYR 0.009 0.001 TYR B 143 ARG 0.005 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 728) hydrogen bonds : angle 4.90166 ( 1878) covalent geometry : bond 0.00329 (14820) covalent geometry : angle 0.60246 (20105) Misc. bond : bond 0.00059 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 2.029 Fit side-chains REVERT: C 355 MET cc_start: 0.8755 (mtp) cc_final: 0.8341 (mtt) REVERT: A 360 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: B 92 ASN cc_start: 0.8639 (m110) cc_final: 0.8323 (m110) REVERT: B 100 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 125 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: B 224 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7900 (mp0) REVERT: B 361 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7598 (mt-10) REVERT: D 121 GLN cc_start: 0.8734 (tt0) cc_final: 0.8422 (tm-30) REVERT: E 51 ASP cc_start: 0.7749 (t0) cc_final: 0.7525 (p0) REVERT: E 77 THR cc_start: 0.9087 (m) cc_final: 0.8774 (p) REVERT: E 311 ASP cc_start: 0.8544 (m-30) cc_final: 0.8189 (m-30) outliers start: 28 outliers final: 12 residues processed: 215 average time/residue: 1.5277 time to fit residues: 356.5716 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095605 restraints weight = 14847.809| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.25 r_work: 0.2973 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14825 Z= 0.111 Angle : 0.567 7.522 20105 Z= 0.273 Chirality : 0.044 0.166 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.152 173.117 2057 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.42 % Allowed : 9.61 % Favored : 88.97 % 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: 1.55 (0.20), residues: 1795 helix: 0.84 (0.19), residues: 775 sheet: -0.13 (0.25), residues: 345 loop : 2.34 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 173 PHE 0.007 0.001 PHE B 255 TYR 0.006 0.001 TYR B 143 ARG 0.006 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 728) hydrogen bonds : angle 4.67189 ( 1878) covalent geometry : bond 0.00239 (14820) covalent geometry : angle 0.56739 (20105) Misc. bond : bond 0.00033 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.802 Fit side-chains REVERT: C 355 MET cc_start: 0.8731 (mtp) cc_final: 0.8311 (mtt) REVERT: A 28 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8473 (ttm170) REVERT: A 125 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 92 ASN cc_start: 0.8627 (m110) cc_final: 0.8322 (m110) REVERT: B 100 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 125 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: B 224 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7927 (mp0) REVERT: D 225 ASN cc_start: 0.8212 (t0) cc_final: 0.7898 (m-40) REVERT: E 41 GLN cc_start: 0.6824 (tt0) cc_final: 0.6610 (mm110) REVERT: E 77 THR cc_start: 0.9070 (m) cc_final: 0.8781 (p) outliers start: 22 outliers final: 9 residues processed: 205 average time/residue: 1.5246 time to fit residues: 340.1768 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091872 restraints weight = 14923.790| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.26 r_work: 0.2908 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14825 Z= 0.254 Angle : 0.678 8.542 20105 Z= 0.339 Chirality : 0.050 0.199 2230 Planarity : 0.004 0.036 2565 Dihedral : 12.704 168.491 2055 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.61 % Allowed : 8.77 % Favored : 89.61 % 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: 1.28 (0.20), residues: 1795 helix: 0.65 (0.19), residues: 790 sheet: -0.34 (0.26), residues: 315 loop : 2.09 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 340 HIS 0.006 0.002 HIS D 173 PHE 0.014 0.002 PHE C 262 TYR 0.008 0.001 TYR E 143 ARG 0.005 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 728) hydrogen bonds : angle 5.00904 ( 1878) covalent geometry : bond 0.00589 (14820) covalent geometry : angle 0.67787 (20105) Misc. bond : bond 0.00137 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.812 Fit side-chains REVERT: C 355 MET cc_start: 0.8772 (mtp) cc_final: 0.8326 (mtt) REVERT: A 28 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8478 (ttm170) REVERT: A 125 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 234 SER cc_start: 0.8431 (p) cc_final: 0.8221 (t) REVERT: A 326 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (pttm) REVERT: B 100 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 125 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 224 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7910 (mp0) REVERT: D 121 GLN cc_start: 0.8681 (tt0) cc_final: 0.8379 (tm-30) REVERT: E 41 GLN cc_start: 0.6762 (tt0) cc_final: 0.6507 (mp-120) REVERT: E 311 ASP cc_start: 0.8579 (m-30) cc_final: 0.8203 (m-30) REVERT: E 314 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8132 (tt0) outliers start: 25 outliers final: 13 residues processed: 201 average time/residue: 1.5709 time to fit residues: 343.2531 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092271 restraints weight = 14838.621| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.26 r_work: 0.2916 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14825 Z= 0.215 Angle : 0.654 8.427 20105 Z= 0.325 Chirality : 0.049 0.194 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.624 168.860 2055 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 9.35 % Favored : 89.23 % 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: 1.29 (0.20), residues: 1795 helix: 0.69 (0.19), residues: 790 sheet: -0.34 (0.27), residues: 315 loop : 2.08 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 340 HIS 0.006 0.002 HIS C 161 PHE 0.013 0.002 PHE C 262 TYR 0.007 0.001 TYR E 143 ARG 0.005 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 728) hydrogen bonds : angle 4.95434 ( 1878) covalent geometry : bond 0.00496 (14820) covalent geometry : angle 0.65401 (20105) Misc. bond : bond 0.00128 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.718 Fit side-chains REVERT: C 354 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: C 355 MET cc_start: 0.8762 (mtp) cc_final: 0.8302 (mtt) REVERT: A 28 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8455 (ttm170) REVERT: A 125 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 326 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7923 (pttm) REVERT: B 100 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 125 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: B 224 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7917 (mp0) REVERT: D 225 ASN cc_start: 0.8281 (t0) cc_final: 0.7874 (m-40) REVERT: D 314 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8328 (tp40) REVERT: E 41 GLN cc_start: 0.6750 (tt0) cc_final: 0.6497 (mm-40) REVERT: E 311 ASP cc_start: 0.8580 (m-30) cc_final: 0.8223 (m-30) REVERT: E 314 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8171 (tt0) outliers start: 22 outliers final: 14 residues processed: 193 average time/residue: 1.5235 time to fit residues: 320.7543 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 0.0050 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094680 restraints weight = 14838.189| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.28 r_work: 0.2957 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14825 Z= 0.125 Angle : 0.582 7.797 20105 Z= 0.282 Chirality : 0.045 0.175 2230 Planarity : 0.003 0.035 2565 Dihedral : 12.257 171.255 2055 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.35 % Allowed : 9.74 % Favored : 88.90 % 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: 1.66 (0.20), residues: 1795 helix: 0.97 (0.19), residues: 775 sheet: -0.11 (0.25), residues: 345 loop : 2.35 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS B 173 PHE 0.008 0.001 PHE C 31 TYR 0.007 0.001 TYR A 143 ARG 0.005 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 728) hydrogen bonds : angle 4.72456 ( 1878) covalent geometry : bond 0.00275 (14820) covalent geometry : angle 0.58157 (20105) Misc. bond : bond 0.00058 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.859 Fit side-chains REVERT: C 100 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: C 355 MET cc_start: 0.8737 (mtp) cc_final: 0.8277 (mtt) REVERT: A 28 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8441 (ttm170) REVERT: A 125 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 227 MET cc_start: 0.8517 (mmm) cc_final: 0.8048 (mmm) REVERT: B 92 ASN cc_start: 0.8664 (m110) cc_final: 0.8312 (m110) REVERT: B 100 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 125 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: D 121 GLN cc_start: 0.8687 (tt0) cc_final: 0.8386 (tm-30) REVERT: D 225 ASN cc_start: 0.8228 (t0) cc_final: 0.7877 (m-40) REVERT: D 314 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8310 (tp40) REVERT: D 328 LYS cc_start: 0.8807 (tppt) cc_final: 0.8493 (mmmt) REVERT: E 41 GLN cc_start: 0.6691 (tt0) cc_final: 0.6373 (mp10) REVERT: E 77 THR cc_start: 0.9092 (m) cc_final: 0.8839 (p) REVERT: E 311 ASP cc_start: 0.8536 (m-30) cc_final: 0.8213 (m-30) REVERT: E 314 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8215 (tt0) outliers start: 21 outliers final: 11 residues processed: 192 average time/residue: 1.5320 time to fit residues: 319.9832 Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094439 restraints weight = 14769.905| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.28 r_work: 0.2954 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14825 Z= 0.127 Angle : 0.586 7.762 20105 Z= 0.284 Chirality : 0.045 0.174 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.240 172.551 2055 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 9.61 % Favored : 88.77 % 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: 1.71 (0.20), residues: 1795 helix: 1.04 (0.19), residues: 775 sheet: -0.09 (0.25), residues: 345 loop : 2.36 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.006 0.001 HIS B 173 PHE 0.008 0.001 PHE C 262 TYR 0.006 0.001 TYR A 294 ARG 0.007 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 728) hydrogen bonds : angle 4.69556 ( 1878) covalent geometry : bond 0.00280 (14820) covalent geometry : angle 0.58578 (20105) Misc. bond : bond 0.00037 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.692 Fit side-chains REVERT: C 354 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: C 355 MET cc_start: 0.8739 (mtp) cc_final: 0.8278 (mtt) REVERT: A 28 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8489 (ttm170) REVERT: A 125 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 227 MET cc_start: 0.8501 (mmm) cc_final: 0.8027 (mmm) REVERT: B 92 ASN cc_start: 0.8668 (m110) cc_final: 0.8322 (m110) REVERT: B 100 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 125 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: D 121 GLN cc_start: 0.8682 (tt0) cc_final: 0.8359 (tm-30) REVERT: D 225 ASN cc_start: 0.8239 (t0) cc_final: 0.7882 (m-40) REVERT: D 314 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: D 328 LYS cc_start: 0.8807 (tppt) cc_final: 0.8490 (mmmt) REVERT: E 41 GLN cc_start: 0.6676 (tt0) cc_final: 0.6418 (mp10) REVERT: E 77 THR cc_start: 0.9089 (m) cc_final: 0.8843 (p) REVERT: E 100 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: E 311 ASP cc_start: 0.8511 (m-30) cc_final: 0.8197 (m-30) REVERT: E 314 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8215 (tt0) outliers start: 25 outliers final: 13 residues processed: 196 average time/residue: 1.5045 time to fit residues: 321.2644 Evaluate side-chains 193 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092382 restraints weight = 14698.599| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.27 r_work: 0.2916 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14825 Z= 0.210 Angle : 0.651 8.396 20105 Z= 0.323 Chirality : 0.048 0.192 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.604 168.742 2055 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.35 % Allowed : 10.19 % Favored : 88.45 % 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: 1.42 (0.20), residues: 1795 helix: 0.83 (0.19), residues: 790 sheet: -0.31 (0.27), residues: 315 loop : 2.13 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 340 HIS 0.006 0.002 HIS C 161 PHE 0.012 0.002 PHE C 262 TYR 0.008 0.001 TYR A 69 ARG 0.006 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 728) hydrogen bonds : angle 4.91714 ( 1878) covalent geometry : bond 0.00484 (14820) covalent geometry : angle 0.65113 (20105) Misc. bond : bond 0.00107 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.959 Fit side-chains REVERT: C 95 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: C 354 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: C 355 MET cc_start: 0.8763 (mtp) cc_final: 0.8301 (mtt) REVERT: A 28 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8494 (ttm170) REVERT: A 125 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 100 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 125 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: D 225 ASN cc_start: 0.8298 (t0) cc_final: 0.7899 (m-40) REVERT: D 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8291 (tp40) REVERT: E 41 GLN cc_start: 0.6715 (tt0) cc_final: 0.6407 (mp10) REVERT: E 77 THR cc_start: 0.9096 (m) cc_final: 0.8819 (p) REVERT: E 100 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: E 311 ASP cc_start: 0.8561 (m-30) cc_final: 0.8224 (m-30) REVERT: E 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8175 (tt0) outliers start: 21 outliers final: 11 residues processed: 193 average time/residue: 1.6023 time to fit residues: 336.5664 Evaluate side-chains 193 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093949 restraints weight = 14849.936| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.27 r_work: 0.2942 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14825 Z= 0.141 Angle : 0.601 7.937 20105 Z= 0.293 Chirality : 0.045 0.178 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.330 170.625 2055 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.23 % Allowed : 10.32 % Favored : 88.45 % 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: 1.69 (0.20), residues: 1795 helix: 1.03 (0.19), residues: 775 sheet: -0.09 (0.25), residues: 345 loop : 2.33 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.006 0.001 HIS B 173 PHE 0.009 0.001 PHE C 262 TYR 0.006 0.001 TYR E 91 ARG 0.007 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 728) hydrogen bonds : angle 4.76995 ( 1878) covalent geometry : bond 0.00315 (14820) covalent geometry : angle 0.60114 (20105) Misc. bond : bond 0.00055 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 3.516 Fit side-chains REVERT: C 354 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: C 355 MET cc_start: 0.8748 (mtp) cc_final: 0.8287 (mtt) REVERT: A 28 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8468 (ttm170) REVERT: A 125 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: B 100 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 125 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: D 121 GLN cc_start: 0.8668 (tt0) cc_final: 0.8362 (tm-30) REVERT: D 222 ASP cc_start: 0.8533 (t0) cc_final: 0.8284 (t0) REVERT: D 225 ASN cc_start: 0.8250 (t0) cc_final: 0.7890 (m-40) REVERT: D 314 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8288 (tp40) REVERT: D 328 LYS cc_start: 0.8813 (tppt) cc_final: 0.8495 (mmmt) REVERT: E 41 GLN cc_start: 0.6712 (tt0) cc_final: 0.6428 (mp10) REVERT: E 77 THR cc_start: 0.9096 (m) cc_final: 0.8846 (p) REVERT: E 100 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: E 311 ASP cc_start: 0.8528 (m-30) cc_final: 0.8209 (m-30) REVERT: E 314 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8213 (tt0) outliers start: 19 outliers final: 12 residues processed: 188 average time/residue: 2.2276 time to fit residues: 457.3417 Evaluate side-chains 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095693 restraints weight = 14938.671| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.28 r_work: 0.2977 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14825 Z= 0.105 Angle : 0.567 7.456 20105 Z= 0.271 Chirality : 0.044 0.164 2230 Planarity : 0.003 0.035 2565 Dihedral : 12.068 173.037 2055 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.16 % Allowed : 10.26 % Favored : 88.58 % 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 (0.20), residues: 1795 helix: 1.19 (0.19), residues: 775 sheet: -0.06 (0.25), residues: 345 loop : 2.38 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS B 173 PHE 0.008 0.001 PHE C 31 TYR 0.006 0.001 TYR E 91 ARG 0.007 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 728) hydrogen bonds : angle 4.60791 ( 1878) covalent geometry : bond 0.00227 (14820) covalent geometry : angle 0.56698 (20105) Misc. bond : bond 0.00027 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14141.06 seconds wall clock time: 245 minutes 44.76 seconds (14744.76 seconds total)