Starting phenix.real_space_refine on Wed Mar 4 16:58:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8v_24321/03_2026/7r8v_24321.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9360 2.51 5 N 2510 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14845 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A, C, D, E Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N AVAL B 45 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.20 residue: pdb=" N AGLY B 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.50 residue: pdb=" N AMET B 47 " occ=0.80 ... (14 atoms not shown) pdb=" CE BMET B 47 " occ=0.20 residue: pdb=" N AGLY B 48 " occ=0.80 ... (6 atoms not shown) pdb=" O BGLY B 48 " occ=0.20 residue: pdb=" N AGLN B 49 " occ=0.80 ... (16 atoms not shown) pdb=" NE2BGLN B 49 " occ=0.20 residue: pdb=" N ALYS B 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 50 " occ=0.50 residue: pdb=" N AVAL A 45 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BVAL A 45 " occ=0.20 residue: pdb=" N AGLY A 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 46 " occ=0.50 residue: pdb=" N AMET A 47 " occ=0.80 ... (14 atoms not shown) pdb=" CE BMET A 47 " occ=0.20 residue: pdb=" N AGLY A 48 " occ=0.80 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.20 residue: pdb=" N AGLN A 49 " occ=0.80 ... (16 atoms not shown) pdb=" NE2BGLN A 49 " occ=0.20 residue: pdb=" N ALYS A 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 50 " occ=0.50 ... (remaining 18 not shown) Time building chain proxies: 2.94, per 1000 atoms: 0.20 Number of scatterers: 14845 At special positions: 0 Unit cell: (89.61, 93.73, 196.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 10 15.00 Mg 5 11.99 O 2850 8.00 N 2510 7.00 C 9360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 28 sheets defined 51.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.027A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.577A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 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 289 through 295 removed outlier: 3.535A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) 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 348 Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.586A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.010A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.028A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.576A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 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 289 through 295 removed outlier: 3.535A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) 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 348 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.586A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.010A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.027A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.576A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 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 289 through 295 removed outlier: 3.535A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) 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 348 Processing helix chain 'C' and resid 349 through 356 removed outlier: 3.586A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.010A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.027A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.577A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 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 289 through 295 removed outlier: 3.535A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) 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 348 Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.586A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.010A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.028A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.576A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 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 289 through 295 removed outlier: 3.535A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.193A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) 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 348 Processing helix chain 'E' and resid 349 through 356 removed outlier: 3.586A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.010A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.796A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.073A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.492A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 removed outlier: 4.066A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA8, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.796A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.492A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.795A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.492A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.796A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'D' and resid 41 through 42 removed outlier: 4.082A pdb=" N GLN D 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) 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 176 through 178 removed outlier: 6.492A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.795A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.492A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 238 through 241 738 hydrogen bonds defined for protein. 1884 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: 2.19 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4833 1.34 - 1.46: 3130 1.46 - 1.58: 6997 1.58 - 1.69: 15 1.69 - 1.81: 195 Bond restraints: 15170 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.89e+00 ... (remaining 15165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 19860 1.12 - 2.24: 478 2.24 - 3.36: 162 3.36 - 4.48: 50 4.48 - 5.60: 35 Bond angle restraints: 20585 Sorted by residual: angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 114.64 -4.14 1.70e+00 3.46e-01 5.94e+00 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 114.62 -4.12 1.70e+00 3.46e-01 5.88e+00 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 114.60 -4.10 1.70e+00 3.46e-01 5.82e+00 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 114.60 -4.10 1.70e+00 3.46e-01 5.80e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 114.59 -4.09 1.70e+00 3.46e-01 5.80e+00 ... (remaining 20580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 8873 29.98 - 59.95: 222 59.95 - 89.93: 15 89.93 - 119.90: 5 119.90 - 149.88: 10 Dihedral angle restraints: 9125 sinusoidal: 3690 harmonic: 5435 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.13 149.88 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.13 149.87 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.14 149.86 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1278 0.028 - 0.056: 607 0.056 - 0.085: 201 0.085 - 0.113: 152 0.113 - 0.141: 42 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE E 165 " pdb=" N ILE E 165 " pdb=" C ILE E 165 " pdb=" CB ILE E 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 2277 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 366 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO E 367 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 367 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 367 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO B 367 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.018 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 11886 3.18 - 3.75: 22843 3.75 - 4.33: 33491 4.33 - 4.90: 56221 Nonbonded interactions: 124567 Sorted by model distance: nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.028 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.029 2.170 ... (remaining 124562 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' 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=0.20 max=1.00 mean=0.99 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: 8.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.003 0.057 15170 Z= 0.146 Angle : 0.544 5.598 20585 Z= 0.268 Chirality : 0.044 0.141 2280 Planarity : 0.004 0.032 2635 Dihedral : 14.128 149.878 5655 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1870 helix: 0.58 (0.19), residues: 795 sheet: 0.69 (0.29), residues: 325 loop : 0.76 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.008 0.001 TYR A 143 PHE 0.006 0.001 PHE C 255 TRP 0.007 0.001 TRP C 79 HIS 0.002 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00309 (15170) covalent geometry : angle 0.54439 (20585) hydrogen bonds : bond 0.18721 ( 738) hydrogen bonds : angle 6.40820 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.514 Fit side-chains REVERT: A 299 MET cc_start: 0.8577 (mtm) cc_final: 0.8345 (mtm) REVERT: C 123 MET cc_start: 0.9069 (mmt) cc_final: 0.8411 (mmt) REVERT: C 283 MET cc_start: 0.8924 (mmm) cc_final: 0.8703 (mmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.8105 time to fit residues: 160.8749 Evaluate side-chains 125 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS A 101 HIS A 225 ASN A 246 GLN D 101 HIS E 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.088578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.068214 restraints weight = 76423.789| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.33 r_work: 0.2514 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15170 Z= 0.185 Angle : 0.615 6.547 20585 Z= 0.305 Chirality : 0.047 0.156 2280 Planarity : 0.005 0.045 2635 Dihedral : 11.412 149.768 2120 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.14 % Allowed : 5.43 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1870 helix: 0.61 (0.19), residues: 790 sheet: 0.64 (0.28), residues: 340 loop : 0.76 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.012 0.001 TYR E 166 PHE 0.010 0.001 PHE C 375 TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00445 (15170) covalent geometry : angle 0.61477 (20585) hydrogen bonds : bond 0.04427 ( 738) hydrogen bonds : angle 4.94904 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.637 Fit side-chains REVERT: A 44 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8112 (mpt) REVERT: A 107 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: C 95 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8197 (mtt-85) REVERT: C 123 MET cc_start: 0.9174 (mmt) cc_final: 0.8407 (mmt) REVERT: E 326 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8342 (mptp) outliers start: 18 outliers final: 6 residues processed: 148 average time/residue: 0.7946 time to fit residues: 126.2056 Evaluate side-chains 134 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.068661 restraints weight = 65981.802| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.18 r_work: 0.2529 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15170 Z= 0.158 Angle : 0.595 7.081 20585 Z= 0.292 Chirality : 0.046 0.155 2280 Planarity : 0.004 0.040 2635 Dihedral : 11.174 155.163 2120 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.20 % Allowed : 5.93 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1870 helix: 0.67 (0.19), residues: 790 sheet: 0.77 (0.29), residues: 335 loop : 0.73 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.009 0.001 TYR D 69 PHE 0.008 0.001 PHE B 375 TRP 0.011 0.002 TRP D 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00379 (15170) covalent geometry : angle 0.59464 (20585) hydrogen bonds : bond 0.03972 ( 738) hydrogen bonds : angle 4.69788 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.556 Fit side-chains REVERT: B 95 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8484 (mtp85) REVERT: B 360 GLN cc_start: 0.8113 (mp10) cc_final: 0.7805 (pm20) REVERT: A 44 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8195 (mpt) REVERT: A 95 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: A 107 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: C 123 MET cc_start: 0.9171 (mmt) cc_final: 0.8339 (mmt) REVERT: D 176 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8442 (mtm) outliers start: 19 outliers final: 6 residues processed: 138 average time/residue: 0.8028 time to fit residues: 118.7966 Evaluate side-chains 133 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.068512 restraints weight = 70620.027| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.06 r_work: 0.2526 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15170 Z= 0.171 Angle : 0.599 7.357 20585 Z= 0.294 Chirality : 0.047 0.160 2280 Planarity : 0.004 0.043 2635 Dihedral : 11.191 158.204 2120 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.95 % Allowed : 6.75 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1870 helix: 0.66 (0.19), residues: 790 sheet: 0.77 (0.29), residues: 335 loop : 0.74 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 95 TYR 0.010 0.001 TYR E 166 PHE 0.008 0.001 PHE D 31 TRP 0.011 0.002 TRP D 79 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00412 (15170) covalent geometry : angle 0.59893 (20585) hydrogen bonds : bond 0.03967 ( 738) hydrogen bonds : angle 4.64548 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.584 Fit side-chains REVERT: A 44 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8244 (mpt) REVERT: A 95 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7755 (mtp180) REVERT: A 107 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: C 95 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: C 123 MET cc_start: 0.9179 (mmt) cc_final: 0.8330 (mmt) REVERT: D 176 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: D 369 ILE cc_start: 0.9191 (tp) cc_final: 0.8874 (tp) REVERT: E 246 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8883 (mt0) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.8330 time to fit residues: 116.9810 Evaluate side-chains 136 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 137 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.089269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.069621 restraints weight = 60440.662| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.96 r_work: 0.2554 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15170 Z= 0.134 Angle : 0.573 7.073 20585 Z= 0.278 Chirality : 0.045 0.153 2280 Planarity : 0.004 0.042 2635 Dihedral : 11.095 158.901 2120 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.95 % Allowed : 7.19 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1870 helix: 0.77 (0.19), residues: 790 sheet: 0.77 (0.29), residues: 335 loop : 0.80 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.008 0.001 TYR C 306 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00319 (15170) covalent geometry : angle 0.57267 (20585) hydrogen bonds : bond 0.03497 ( 738) hydrogen bonds : angle 4.54419 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.553 Fit side-chains REVERT: B 246 GLN cc_start: 0.9120 (mt0) cc_final: 0.8869 (mt0) REVERT: A 44 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8229 (mpt) REVERT: A 95 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: A 107 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: C 123 MET cc_start: 0.9166 (mmt) cc_final: 0.8339 (mmt) REVERT: C 372 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8060 (ptp90) REVERT: D 95 ARG cc_start: 0.8730 (mtt-85) cc_final: 0.8506 (mtp180) REVERT: D 176 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: D 369 ILE cc_start: 0.9165 (tp) cc_final: 0.8898 (tp) REVERT: E 246 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8859 (mt0) REVERT: E 326 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8415 (mptp) outliers start: 15 outliers final: 5 residues processed: 135 average time/residue: 0.8314 time to fit residues: 120.4086 Evaluate side-chains 133 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.088554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.068675 restraints weight = 71112.473| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.19 r_work: 0.2518 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15170 Z= 0.160 Angle : 0.585 7.250 20585 Z= 0.285 Chirality : 0.046 0.157 2280 Planarity : 0.004 0.040 2635 Dihedral : 11.128 160.644 2120 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 7.32 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1870 helix: 0.74 (0.19), residues: 790 sheet: 0.70 (0.27), residues: 365 loop : 0.82 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 95 TYR 0.009 0.001 TYR D 69 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00384 (15170) covalent geometry : angle 0.58482 (20585) hydrogen bonds : bond 0.03768 ( 738) hydrogen bonds : angle 4.55881 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.554 Fit side-chains REVERT: B 95 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8342 (mtt-85) REVERT: B 360 GLN cc_start: 0.8089 (mp10) cc_final: 0.7875 (pm20) REVERT: A 44 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8241 (mpt) REVERT: A 95 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: A 107 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: C 123 MET cc_start: 0.9180 (mmt) cc_final: 0.8359 (mmt) REVERT: D 176 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: D 369 ILE cc_start: 0.9179 (tp) cc_final: 0.8883 (tp) REVERT: E 246 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8862 (mt0) outliers start: 15 outliers final: 6 residues processed: 133 average time/residue: 0.8312 time to fit residues: 118.6502 Evaluate side-chains 133 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.088624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.068794 restraints weight = 63018.001| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.02 r_work: 0.2539 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15170 Z= 0.157 Angle : 0.587 8.281 20585 Z= 0.285 Chirality : 0.046 0.156 2280 Planarity : 0.004 0.041 2635 Dihedral : 11.121 160.903 2120 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.95 % Allowed : 7.44 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1870 helix: 0.76 (0.19), residues: 790 sheet: 0.71 (0.27), residues: 365 loop : 0.82 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 95 TYR 0.009 0.001 TYR D 69 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00376 (15170) covalent geometry : angle 0.58716 (20585) hydrogen bonds : bond 0.03701 ( 738) hydrogen bonds : angle 4.55092 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.410 Fit side-chains REVERT: B 95 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8330 (mtt-85) REVERT: B 360 GLN cc_start: 0.8055 (mp10) cc_final: 0.7844 (pm20) REVERT: A 44 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8251 (mpt) REVERT: A 95 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7728 (mtp180) REVERT: A 107 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: C 123 MET cc_start: 0.9191 (mmt) cc_final: 0.8367 (mmt) REVERT: D 176 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8443 (mtm) REVERT: D 369 ILE cc_start: 0.9195 (tp) cc_final: 0.8898 (tp) REVERT: E 246 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8839 (mt0) outliers start: 15 outliers final: 6 residues processed: 126 average time/residue: 0.8235 time to fit residues: 111.3079 Evaluate side-chains 132 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.068126 restraints weight = 75490.973| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.33 r_work: 0.2503 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15170 Z= 0.170 Angle : 0.593 7.372 20585 Z= 0.289 Chirality : 0.046 0.159 2280 Planarity : 0.004 0.042 2635 Dihedral : 11.156 161.962 2120 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.95 % Allowed : 7.38 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1870 helix: 0.73 (0.19), residues: 790 sheet: 0.72 (0.27), residues: 365 loop : 0.80 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 95 TYR 0.010 0.001 TYR D 69 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00409 (15170) covalent geometry : angle 0.59300 (20585) hydrogen bonds : bond 0.03834 ( 738) hydrogen bonds : angle 4.56826 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.563 Fit side-chains REVERT: B 95 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8355 (mtt-85) REVERT: B 360 GLN cc_start: 0.8079 (mp10) cc_final: 0.7863 (pm20) REVERT: A 44 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8261 (mpt) REVERT: A 95 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: A 107 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: C 123 MET cc_start: 0.9208 (mmt) cc_final: 0.8359 (mmt) REVERT: C 250 ILE cc_start: 0.8975 (mp) cc_final: 0.8487 (tt) REVERT: D 176 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: D 369 ILE cc_start: 0.9192 (tp) cc_final: 0.8904 (tp) REVERT: E 246 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8878 (mt0) outliers start: 15 outliers final: 6 residues processed: 131 average time/residue: 0.8267 time to fit residues: 116.1492 Evaluate side-chains 130 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 121 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 106 optimal weight: 0.0370 chunk 171 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.089288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.070009 restraints weight = 63943.433| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.95 r_work: 0.2555 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15170 Z= 0.130 Angle : 0.572 7.033 20585 Z= 0.277 Chirality : 0.045 0.154 2280 Planarity : 0.004 0.040 2635 Dihedral : 11.065 161.492 2120 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.76 % Allowed : 7.95 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1870 helix: 0.82 (0.19), residues: 790 sheet: 0.71 (0.28), residues: 365 loop : 0.85 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 95 TYR 0.008 0.001 TYR C 306 PHE 0.009 0.001 PHE D 31 TRP 0.010 0.001 TRP B 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00309 (15170) covalent geometry : angle 0.57213 (20585) hydrogen bonds : bond 0.03401 ( 738) hydrogen bonds : angle 4.49519 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.588 Fit side-chains REVERT: B 95 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8335 (mtt-85) REVERT: A 44 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8224 (mpt) REVERT: A 95 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: A 107 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: C 95 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8380 (mtt-85) REVERT: C 123 MET cc_start: 0.9194 (mmt) cc_final: 0.8334 (mmt) REVERT: D 176 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8433 (mtm) REVERT: D 276 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8203 (mt-10) REVERT: D 369 ILE cc_start: 0.9222 (tp) cc_final: 0.8937 (tp) REVERT: E 246 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8851 (mt0) outliers start: 12 outliers final: 4 residues processed: 129 average time/residue: 0.8650 time to fit residues: 119.5949 Evaluate side-chains 131 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.0050 chunk 69 optimal weight: 0.9980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.069111 restraints weight = 54582.024| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.77 r_work: 0.2545 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15170 Z= 0.170 Angle : 0.601 7.963 20585 Z= 0.294 Chirality : 0.046 0.156 2280 Planarity : 0.004 0.039 2635 Dihedral : 11.136 162.908 2120 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.63 % Allowed : 8.26 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1870 helix: 0.75 (0.19), residues: 790 sheet: 0.72 (0.28), residues: 365 loop : 0.83 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 95 TYR 0.010 0.001 TYR D 69 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00412 (15170) covalent geometry : angle 0.60061 (20585) hydrogen bonds : bond 0.03814 ( 738) hydrogen bonds : angle 4.54869 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.681 Fit side-chains REVERT: B 95 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8337 (mtt-85) REVERT: A 44 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8236 (mpt) REVERT: A 95 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: A 107 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: C 95 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8379 (mtt-85) REVERT: C 123 MET cc_start: 0.9198 (mmt) cc_final: 0.8349 (mmt) REVERT: C 250 ILE cc_start: 0.8963 (mp) cc_final: 0.8479 (tt) REVERT: D 176 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8425 (mtm) REVERT: D 328 LYS cc_start: 0.8791 (mptt) cc_final: 0.8511 (mmtm) REVERT: D 369 ILE cc_start: 0.9216 (tp) cc_final: 0.8941 (tp) REVERT: E 246 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8847 (mt0) outliers start: 10 outliers final: 4 residues processed: 127 average time/residue: 0.8550 time to fit residues: 116.4843 Evaluate side-chains 129 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 0.0000 chunk 159 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.089651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.069418 restraints weight = 81346.071| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.47 r_work: 0.2536 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15170 Z= 0.121 Angle : 0.574 8.304 20585 Z= 0.279 Chirality : 0.045 0.152 2280 Planarity : 0.004 0.041 2635 Dihedral : 11.027 161.530 2120 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 7.89 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1870 helix: 0.85 (0.19), residues: 790 sheet: 0.71 (0.28), residues: 365 loop : 0.90 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 95 TYR 0.008 0.001 TYR C 306 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.001 TRP E 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (15170) covalent geometry : angle 0.57363 (20585) hydrogen bonds : bond 0.03285 ( 738) hydrogen bonds : angle 4.46385 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.55 seconds wall clock time: 79 minutes 36.62 seconds (4776.62 seconds total)