Starting phenix.real_space_refine on Tue Dec 31 06:42:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_24321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_24321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_24321.map" model { file = "/net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_24321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8v_24321/12_2024/7r8v_24321.cif" } resolution = 2.82 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= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14845 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B, E, D 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: 9.92, per 1000 atoms: 0.67 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: 3.81 Conformation dependent library (CDL) restraints added in 3.7 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: 2.02 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: 5.17 Time building geometry restraints manager: 4.40 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'B' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'C' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) } 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: 8.350 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.890 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- 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= 0.194 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 (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: 0.86 (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 TRP 0.007 0.001 TRP C 79 HIS 0.002 0.001 HIS C 161 PHE 0.006 0.001 PHE C 255 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG A 28 *********************** 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 : 1.613 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: 0.8412 (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: 1.8521 time to fit residues: 367.5885 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 : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1132 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= 0.284 Angle : 0.609 6.560 20585 Z= 0.303 Chirality : 0.047 0.157 2280 Planarity : 0.005 0.043 2635 Dihedral : 11.397 149.857 2120 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.20 % Allowed : 5.30 % Favored : 93.50 % 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: 0.88 (0.20), residues: 1870 helix: 0.63 (0.19), residues: 790 sheet: 0.65 (0.28), residues: 340 loop : 0.77 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.008 0.001 PHE B 375 TYR 0.012 0.001 TYR E 166 ARG 0.010 0.001 ARG C 95 *********************** 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: 19 poor density : 143 time to evaluate : 1.585 Fit side-chains REVERT: A 44 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7853 (mpt) REVERT: A 107 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: A 299 MET cc_start: 0.8546 (mtm) cc_final: 0.8309 (mtm) REVERT: C 123 MET cc_start: 0.9075 (mmt) cc_final: 0.8270 (mmt) outliers start: 19 outliers final: 6 residues processed: 148 average time/residue: 1.8144 time to fit residues: 288.5854 Evaluate side-chains 132 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15170 Z= 0.246 Angle : 0.593 7.068 20585 Z= 0.292 Chirality : 0.046 0.154 2280 Planarity : 0.004 0.042 2635 Dihedral : 11.172 154.954 2120 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.07 % Allowed : 6.06 % 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 (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: 0.92 (0.20), residues: 1870 helix: 0.68 (0.19), residues: 790 sheet: 0.65 (0.29), residues: 340 loop : 0.78 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE B 375 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 *********************** 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 148 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.788 Fit side-chains REVERT: A 44 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7905 (mpt) REVERT: A 95 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: A 107 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 299 MET cc_start: 0.8536 (mtm) cc_final: 0.8305 (mtm) REVERT: C 123 MET cc_start: 0.9043 (mmt) cc_final: 0.8190 (mmt) REVERT: D 176 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7860 (mtm) outliers start: 17 outliers final: 4 residues processed: 138 average time/residue: 1.8090 time to fit residues: 268.8855 Evaluate side-chains 130 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 0.1980 chunk 88 optimal weight: 0.0770 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15170 Z= 0.199 Angle : 0.571 6.915 20585 Z= 0.278 Chirality : 0.045 0.153 2280 Planarity : 0.004 0.041 2635 Dihedral : 11.073 156.530 2120 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.88 % Allowed : 7.00 % Favored : 92.11 % 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: 1.02 (0.20), residues: 1870 helix: 0.75 (0.19), residues: 790 sheet: 0.77 (0.29), residues: 335 loop : 0.82 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR C 306 ARG 0.010 0.000 ARG C 95 *********************** 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 137 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.688 Fit side-chains REVERT: A 44 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7871 (mpt) REVERT: A 107 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: C 123 MET cc_start: 0.9029 (mmt) cc_final: 0.8147 (mmt) REVERT: D 176 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7874 (mtm) REVERT: D 369 ILE cc_start: 0.9398 (tp) cc_final: 0.9091 (tp) outliers start: 14 outliers final: 5 residues processed: 129 average time/residue: 1.7861 time to fit residues: 248.9466 Evaluate side-chains 130 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15170 Z= 0.241 Angle : 0.585 7.130 20585 Z= 0.285 Chirality : 0.046 0.157 2280 Planarity : 0.004 0.042 2635 Dihedral : 11.100 158.632 2120 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.82 % Allowed : 7.38 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1870 helix: 0.73 (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 TRP 0.010 0.002 TRP D 79 HIS 0.005 0.001 HIS D 161 PHE 0.007 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 *********************** 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 137 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.714 Fit side-chains REVERT: B 95 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8084 (mtt-85) REVERT: A 44 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7880 (mpt) REVERT: A 95 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7948 (mtp180) REVERT: A 107 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: C 123 MET cc_start: 0.9018 (mmt) cc_final: 0.8135 (mmt) REVERT: D 176 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7868 (mtm) REVERT: D 369 ILE cc_start: 0.9395 (tp) cc_final: 0.9098 (tp) outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 1.7494 time to fit residues: 247.4647 Evaluate side-chains 135 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15170 Z= 0.220 Angle : 0.575 7.082 20585 Z= 0.279 Chirality : 0.046 0.156 2280 Planarity : 0.004 0.045 2635 Dihedral : 11.070 158.931 2120 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (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: 1.04 (0.20), residues: 1870 helix: 0.77 (0.19), residues: 790 sheet: 0.70 (0.27), residues: 365 loop : 0.87 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR D 69 ARG 0.010 0.000 ARG E 95 *********************** 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 141 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.716 Fit side-chains REVERT: B 95 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8108 (mtt-85) REVERT: A 44 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7905 (mpt) REVERT: A 95 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7963 (mtp180) REVERT: A 107 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: C 123 MET cc_start: 0.9010 (mmt) cc_final: 0.8157 (mmt) REVERT: D 176 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: D 369 ILE cc_start: 0.9389 (tp) cc_final: 0.9107 (tp) outliers start: 15 outliers final: 7 residues processed: 133 average time/residue: 1.8016 time to fit residues: 257.9600 Evaluate side-chains 131 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15170 Z= 0.257 Angle : 0.592 7.576 20585 Z= 0.288 Chirality : 0.046 0.159 2280 Planarity : 0.004 0.036 2635 Dihedral : 11.114 160.185 2120 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.07 % Allowed : 7.19 % 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 (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: 1.00 (0.20), residues: 1870 helix: 0.73 (0.19), residues: 790 sheet: 0.71 (0.27), residues: 365 loop : 0.84 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.006 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 *********************** 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 141 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.716 Fit side-chains REVERT: B 95 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8121 (mtt-85) REVERT: A 44 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7938 (mpt) REVERT: A 95 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: A 107 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: C 123 MET cc_start: 0.9004 (mmt) cc_final: 0.8157 (mmt) REVERT: D 176 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7856 (mtm) REVERT: D 369 ILE cc_start: 0.9384 (tp) cc_final: 0.9093 (tp) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 1.8278 time to fit residues: 262.0784 Evaluate side-chains 134 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 C residue 190 MET 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 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15170 Z= 0.239 Angle : 0.587 7.834 20585 Z= 0.286 Chirality : 0.046 0.156 2280 Planarity : 0.004 0.037 2635 Dihedral : 11.099 160.404 2120 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 (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: 1.02 (0.20), residues: 1870 helix: 0.75 (0.19), residues: 790 sheet: 0.71 (0.27), residues: 365 loop : 0.84 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR D 69 ARG 0.010 0.000 ARG C 95 *********************** 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 138 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.667 Fit side-chains REVERT: B 95 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8117 (mtt-85) REVERT: A 44 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7915 (mpt) REVERT: A 95 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: A 107 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: C 123 MET cc_start: 0.9020 (mmt) cc_final: 0.8188 (mmt) REVERT: D 176 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7858 (mtm) REVERT: D 369 ILE cc_start: 0.9405 (tp) cc_final: 0.9108 (tp) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 1.8568 time to fit residues: 259.4809 Evaluate side-chains 131 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 190 MET 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 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15170 Z= 0.254 Angle : 0.596 8.049 20585 Z= 0.291 Chirality : 0.046 0.157 2280 Planarity : 0.004 0.038 2635 Dihedral : 11.119 161.336 2120 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.88 % Allowed : 7.63 % Favored : 91.48 % 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: 1.00 (0.20), residues: 1870 helix: 0.74 (0.19), residues: 790 sheet: 0.72 (0.27), residues: 365 loop : 0.82 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 *********************** 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 135 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 2.142 Fit side-chains REVERT: B 95 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8125 (mtt-85) REVERT: A 44 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7943 (mpt) REVERT: A 95 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7903 (mtp180) REVERT: A 107 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: C 123 MET cc_start: 0.9029 (mmt) cc_final: 0.8158 (mmt) REVERT: C 250 ILE cc_start: 0.8730 (mp) cc_final: 0.8524 (tt) REVERT: D 176 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7853 (mtm) REVERT: D 369 ILE cc_start: 0.9415 (tp) cc_final: 0.9123 (tp) outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 1.9662 time to fit residues: 269.8592 Evaluate side-chains 135 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 190 MET 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 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 116 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 0.042 15170 Z= 0.247 Angle : 0.592 8.156 20585 Z= 0.288 Chirality : 0.046 0.156 2280 Planarity : 0.004 0.038 2635 Dihedral : 11.115 161.695 2120 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.88 % Allowed : 7.57 % Favored : 91.55 % 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: 1.02 (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 TRP 0.010 0.001 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 ********************** 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 136 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.779 Fit side-chains REVERT: B 95 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8139 (mtt-85) REVERT: A 44 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7918 (mpt) REVERT: A 95 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7914 (mtp180) REVERT: A 107 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: C 123 MET cc_start: 0.9027 (mmt) cc_final: 0.8134 (mmt) REVERT: C 250 ILE cc_start: 0.8729 (mp) cc_final: 0.8525 (tt) REVERT: D 176 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7851 (mtm) outliers start: 14 outliers final: 8 residues processed: 128 average time/residue: 1.8740 time to fit residues: 257.9793 Evaluate side-chains 130 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 190 MET 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 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.089005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.069404 restraints weight = 59987.495| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.98 r_work: 0.2549 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15170 Z= 0.233 Angle : 0.589 8.125 20585 Z= 0.287 Chirality : 0.046 0.155 2280 Planarity : 0.004 0.038 2635 Dihedral : 11.098 162.060 2120 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.95 % Allowed : 7.63 % Favored : 91.42 % 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: 1.05 (0.20), residues: 1870 helix: 0.78 (0.19), residues: 790 sheet: 0.72 (0.28), residues: 365 loop : 0.85 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5149.40 seconds wall clock time: 93 minutes 20.80 seconds (5600.80 seconds total)