Starting phenix.real_space_refine on Mon Nov 18 01:57:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_15104.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_15104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_15104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_15104.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2r_15104/11_2024/8a2r_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-5513/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: 8.10, per 1000 atoms: 0.54 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: 4.00 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: 2.43 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: 6.47 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.450 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.950 Find NCS groups from input model: 0.590 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.150 ------------------------------------------------------------------------------- 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 : 0.005 0.086 14820 Z= 0.308 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 *********************** 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 : 1.797 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: 1.6180 time to fit residues: 487.2537 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 : 1.868 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14820 Z= 0.246 Angle : 0.630 8.098 20105 Z= 0.314 Chirality : 0.046 0.198 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.451 172.042 2058 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.45 % Favored : 98.44 % Rotamer: Outliers : 2.06 % Allowed : 7.23 % 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: 0.45 (0.19), residues: 1795 helix: -0.27 (0.17), residues: 790 sheet: -0.32 (0.24), residues: 345 loop : 1.86 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS C 161 PHE 0.010 0.001 PHE A 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG A 206 *********************** 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: 32 poor density : 208 time to evaluate : 1.786 Fit side-chains REVERT: C 355 MET cc_start: 0.8187 (mtp) cc_final: 0.7768 (mtt) REVERT: B 92 ASN cc_start: 0.8374 (m110) cc_final: 0.8082 (m110) REVERT: B 100 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 224 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7475 (mp0) REVERT: D 121 GLN cc_start: 0.8298 (tt0) cc_final: 0.8049 (tm-30) outliers start: 32 outliers final: 13 residues processed: 224 average time/residue: 1.5652 time to fit residues: 381.3393 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 328 LYS Chi-restraints excluded: chain A residue 374 CYS 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 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 90 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14820 Z= 0.329 Angle : 0.665 8.546 20105 Z= 0.333 Chirality : 0.049 0.202 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.713 168.541 2058 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % Rotamer: Outliers : 2.06 % Allowed : 7.55 % Favored : 90.39 % 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: 0.98 (0.20), residues: 1795 helix: 0.33 (0.18), residues: 790 sheet: -0.20 (0.25), residues: 345 loop : 2.00 (0.26), residues: 660 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 0.009 0.001 TYR B 143 ARG 0.004 0.001 ARG C 28 *********************** 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 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.681 Fit side-chains REVERT: C 355 MET cc_start: 0.8163 (mtp) cc_final: 0.7721 (mtt) REVERT: A 121 GLN cc_start: 0.8000 (tt0) cc_final: 0.7378 (tm-30) REVERT: A 125 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 224 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7581 (mp0) REVERT: B 361 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 121 GLN cc_start: 0.8324 (tt0) cc_final: 0.8077 (tm-30) outliers start: 32 outliers final: 17 residues processed: 217 average time/residue: 1.5330 time to fit residues: 362.3237 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 326 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 178 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14820 Z= 0.383 Angle : 0.690 8.704 20105 Z= 0.347 Chirality : 0.051 0.205 2230 Planarity : 0.004 0.037 2565 Dihedral : 12.816 168.573 2058 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.74 % Allowed : 8.65 % 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: 1.08 (0.20), residues: 1795 helix: 0.47 (0.19), residues: 790 sheet: -0.36 (0.26), residues: 315 loop : 1.97 (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 C 161 PHE 0.015 0.002 PHE C 262 TYR 0.009 0.001 TYR E 143 ARG 0.004 0.001 ARG E 177 *********************** 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 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.617 Fit side-chains REVERT: C 354 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: C 355 MET cc_start: 0.8163 (mtp) cc_final: 0.7691 (mtt) REVERT: A 121 GLN cc_start: 0.8041 (tt0) cc_final: 0.7378 (tm-30) REVERT: A 125 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 224 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7583 (mp0) REVERT: B 361 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7645 (mt-10) REVERT: E 314 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7948 (tt0) outliers start: 27 outliers final: 20 residues processed: 203 average time/residue: 1.6132 time to fit residues: 356.0741 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 326 LYS Chi-restraints excluded: chain C residue 354 GLN 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 328 LYS Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 51 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14820 Z= 0.173 Angle : 0.585 7.794 20105 Z= 0.284 Chirality : 0.045 0.172 2230 Planarity : 0.003 0.035 2565 Dihedral : 12.308 170.761 2058 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 9.42 % Favored : 89.10 % 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: 0.87 (0.19), residues: 775 sheet: -0.14 (0.25), residues: 345 loop : 2.31 (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 0.003 0.000 ARG C 28 *********************** 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 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 1.849 Fit side-chains REVERT: C 355 MET cc_start: 0.8140 (mtp) cc_final: 0.7663 (mtt) REVERT: A 28 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: A 121 GLN cc_start: 0.7953 (tt0) cc_final: 0.7268 (tt0) REVERT: A 125 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: B 92 ASN cc_start: 0.8391 (m110) cc_final: 0.8077 (m110) REVERT: B 361 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 314 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8001 (tp40) REVERT: E 41 GLN cc_start: 0.5818 (mm110) cc_final: 0.5377 (mp10) outliers start: 23 outliers final: 9 residues processed: 197 average time/residue: 1.6201 time to fit residues: 346.1098 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 323 SER Chi-restraints excluded: chain A residue 374 CYS 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 374 CYS Chi-restraints excluded: chain E residue 96 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 58 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14820 Z= 0.340 Angle : 0.667 8.510 20105 Z= 0.332 Chirality : 0.049 0.199 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.690 168.577 2056 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.61 % Allowed : 9.68 % Favored : 88.71 % 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: 1.33 (0.20), residues: 1795 helix: 0.72 (0.19), residues: 790 sheet: -0.32 (0.27), residues: 315 loop : 2.10 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 A 69 ARG 0.003 0.001 ARG E 177 *********************** 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 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.706 Fit side-chains REVERT: C 95 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6951 (mmp80) REVERT: C 355 MET cc_start: 0.8152 (mtp) cc_final: 0.7660 (mtt) REVERT: A 28 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: A 125 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: B 361 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7627 (mt-10) REVERT: E 314 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7999 (tt0) outliers start: 25 outliers final: 13 residues processed: 194 average time/residue: 1.5524 time to fit residues: 327.3734 Evaluate side-chains 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG 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 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS 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 370 VAL 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 167 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14820 Z= 0.133 Angle : 0.558 7.404 20105 Z= 0.266 Chirality : 0.043 0.161 2230 Planarity : 0.003 0.035 2565 Dihedral : 12.078 171.306 2056 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.29 % Allowed : 10.00 % Favored : 88.71 % 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: 1.76 (0.20), residues: 1795 helix: 1.10 (0.19), residues: 775 sheet: -0.09 (0.25), residues: 345 loop : 2.38 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS B 173 PHE 0.009 0.001 PHE C 31 TYR 0.006 0.001 TYR E 91 ARG 0.004 0.000 ARG C 28 *********************** 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 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.724 Fit side-chains REVERT: C 95 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6987 (mmp80) REVERT: C 355 MET cc_start: 0.8129 (mtp) cc_final: 0.7641 (mtt) REVERT: A 28 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: A 125 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: B 92 ASN cc_start: 0.8368 (m110) cc_final: 0.8062 (m110) REVERT: D 314 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7993 (tp40) REVERT: E 41 GLN cc_start: 0.5920 (mm110) cc_final: 0.5526 (mp10) REVERT: E 314 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8047 (tt0) outliers start: 20 outliers final: 6 residues processed: 196 average time/residue: 1.6758 time to fit residues: 355.5728 Evaluate side-chains 183 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG 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 374 CYS 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 374 CYS 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 107 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.005 0.046 14820 Z= 0.333 Angle : 0.660 8.460 20105 Z= 0.328 Chirality : 0.049 0.198 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.620 168.972 2055 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.35 % Allowed : 10.45 % Favored : 88.19 % 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: 1.46 (0.20), residues: 1795 helix: 0.85 (0.19), residues: 790 sheet: -0.30 (0.27), residues: 315 loop : 2.16 (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 0.012 0.002 PHE C 262 TYR 0.008 0.001 TYR A 69 ARG 0.003 0.001 ARG B 206 *********************** 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 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.650 Fit side-chains REVERT: C 95 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6913 (mmp80) REVERT: C 354 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7902 (pt0) REVERT: C 355 MET cc_start: 0.8151 (mtp) cc_final: 0.7657 (mtt) REVERT: A 28 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: A 125 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: D 314 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7977 (tp40) REVERT: E 41 GLN cc_start: 0.5998 (mm110) cc_final: 0.5604 (mp10) REVERT: E 100 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: E 314 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8009 (tt0) outliers start: 21 outliers final: 10 residues processed: 183 average time/residue: 1.6185 time to fit residues: 321.2434 Evaluate side-chains 183 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 323 SER Chi-restraints excluded: chain A residue 374 CYS 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 314 GLN 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 350 SER 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 157 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14820 Z= 0.236 Angle : 0.618 8.171 20105 Z= 0.303 Chirality : 0.046 0.186 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.438 169.999 2055 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 10.58 % Favored : 88.13 % 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: 1.50 (0.20), residues: 1795 helix: 0.88 (0.19), residues: 790 sheet: -0.12 (0.25), residues: 345 loop : 2.20 (0.26), residues: 660 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 0.010 0.001 PHE C 262 TYR 0.007 0.001 TYR D 188 ARG 0.004 0.000 ARG C 28 *********************** 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 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.760 Fit side-chains REVERT: C 95 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6915 (mmp80) REVERT: C 354 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: C 355 MET cc_start: 0.8145 (mtp) cc_final: 0.7646 (mtt) REVERT: A 28 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: A 125 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: B 361 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 314 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7988 (tp40) REVERT: E 100 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: E 314 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8040 (tt0) outliers start: 20 outliers final: 10 residues processed: 185 average time/residue: 1.6245 time to fit residues: 325.7039 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 323 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS 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 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 350 SER 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 170 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14820 Z= 0.183 Angle : 0.592 7.826 20105 Z= 0.287 Chirality : 0.045 0.176 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.257 172.081 2055 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.10 % Allowed : 10.84 % Favored : 88.06 % 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: 1.72 (0.20), residues: 1795 helix: 1.06 (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 0.006 0.001 HIS B 173 PHE 0.008 0.001 PHE C 262 TYR 0.007 0.001 TYR A 143 ARG 0.007 0.000 ARG C 28 ********************** 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 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.774 Fit side-chains REVERT: C 95 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6943 (mmp80) REVERT: C 355 MET cc_start: 0.8133 (mtp) cc_final: 0.7641 (mtt) REVERT: A 28 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: A 125 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: B 361 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7610 (mt-10) REVERT: D 314 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: E 100 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: E 314 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8058 (tt0) outliers start: 17 outliers final: 8 residues processed: 182 average time/residue: 1.6483 time to fit residues: 325.2350 Evaluate side-chains 179 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS 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 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 152 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.116418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.094364 restraints weight = 14738.428| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.27 r_work: 0.2950 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14820 Z= 0.187 Angle : 0.594 7.843 20105 Z= 0.289 Chirality : 0.045 0.177 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.257 172.747 2055 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 11.03 % Favored : 88.06 % 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: 1.72 (0.20), residues: 1795 helix: 1.07 (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 C 340 HIS 0.006 0.001 HIS B 173 PHE 0.009 0.001 PHE C 262 TYR 0.007 0.001 TYR A 294 ARG 0.008 0.000 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.12 seconds wall clock time: 113 minutes 50.48 seconds (6830.48 seconds total)