Starting phenix.real_space_refine on Fri May 16 09:45:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.map" model { file = "/net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zj1_60135/05_2025/8zj1_60135.cif" } resolution = 4.25 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 100 5.16 5 C 9230 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14625 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.20, per 1000 atoms: 0.63 Number of scatterers: 14625 At special positions: 0 Unit cell: (98.77, 77.19, 193.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 10 15.00 O 2815 8.00 N 2470 7.00 C 9230 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: 3.84 Conformation dependent library (CDL) restraints added in 1.8 seconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 49.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.199A 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 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.725A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.951A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.548A 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 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.681A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.845A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.116A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.866A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.963A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.758A 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 removed outlier: 3.511A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 290 through 296 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.719A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.813A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.775A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.100A 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 172 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 204 through 217 removed outlier: 4.008A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.830A 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 285 removed outlier: 3.541A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.836A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.597A pdb=" N SER F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.757A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.814A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.256A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.884A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.537A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.274A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.866A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.536A pdb=" N ARG F 372 " --> pdb=" O ILE F 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.813A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.774A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.100A 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 172 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 204 through 217 removed outlier: 4.008A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.830A 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 285 removed outlier: 3.541A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.836A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.484A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.567A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 242 removed outlier: 3.728A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.557A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.542A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AB4, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.652A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 242 removed outlier: 4.573A pdb=" N LEU E 242 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.445A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.521A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 238 through 242 removed outlier: 4.408A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.652A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AC9, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.572A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 1752 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: 5.18 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4722 1.33 - 1.45: 2115 1.45 - 1.57: 7923 1.57 - 1.69: 15 1.69 - 1.80: 175 Bond restraints: 14950 Sorted by residual: bond pdb=" N ILE D 287 " pdb=" CA ILE D 287 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.90e+00 bond pdb=" N ILE D 289 " pdb=" CA ILE D 289 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.78e+00 bond pdb=" N ASP D 286 " pdb=" CA ASP D 286 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.73e+00 bond pdb=" N ASP D 288 " pdb=" CA ASP D 288 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.42e-02 4.96e+03 5.78e+00 bond pdb=" CB ARG D 335 " pdb=" CG ARG D 335 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.07e+00 ... (remaining 14945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 19319 1.69 - 3.37: 819 3.37 - 5.06: 117 5.06 - 6.74: 34 6.74 - 8.43: 1 Bond angle restraints: 20290 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" N GLY D 13 " pdb=" CA GLY D 13 " ideal model delta sigma weight residual 121.44 115.69 5.75 1.45e+00 4.76e-01 1.57e+01 angle pdb=" N ASP D 288 " pdb=" CA ASP D 288 " pdb=" C ASP D 288 " ideal model delta sigma weight residual 114.12 109.72 4.40 1.39e+00 5.18e-01 1.00e+01 angle pdb=" CA ASP D 286 " pdb=" C ASP D 286 " pdb=" O ASP D 286 " ideal model delta sigma weight residual 121.56 118.32 3.24 1.09e+00 8.42e-01 8.82e+00 angle pdb=" N CYS D 374 " pdb=" CA CYS D 374 " pdb=" C CYS D 374 " ideal model delta sigma weight residual 110.80 105.38 5.42 2.13e+00 2.20e-01 6.49e+00 angle pdb=" CA LEU F 171 " pdb=" CB LEU F 171 " pdb=" CG LEU F 171 " ideal model delta sigma weight residual 116.30 124.73 -8.43 3.50e+00 8.16e-02 5.80e+00 ... (remaining 20285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8225 17.87 - 35.75: 600 35.75 - 53.62: 144 53.62 - 71.49: 12 71.49 - 89.37: 14 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: 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 -60.00 17.94 -77.93 1 2.00e+01 2.50e-03 1.90e+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 -60.00 14.31 -74.31 1 2.00e+01 2.50e-03 1.75e+01 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 -60.00 14.25 -74.25 1 2.00e+01 2.50e-03 1.75e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1185 0.043 - 0.086: 758 0.086 - 0.129: 286 0.129 - 0.172: 25 0.172 - 0.215: 1 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CB ILE F 71 " pdb=" CA ILE F 71 " pdb=" CG1 ILE F 71 " pdb=" CG2 ILE F 71 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE F 151 " pdb=" CA ILE F 151 " pdb=" CG1 ILE F 151 " pdb=" CG2 ILE F 151 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE D 289 " pdb=" N ILE D 289 " pdb=" C ILE D 289 " pdb=" CB ILE D 289 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 332 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO C 333 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 332 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO D 333 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 332 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO E 333 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 333 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 333 " 0.027 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2050 2.74 - 3.28: 13760 3.28 - 3.82: 23648 3.82 - 4.36: 29908 4.36 - 4.90: 52425 Nonbonded interactions: 121791 Sorted by model distance: nonbonded pdb=" CB SER D 155 " pdb=" CG2 THR D 303 " model vdw 2.196 3.860 nonbonded pdb=" O ASP D 288 " pdb=" OD1 ASP D 288 " model vdw 2.241 3.040 nonbonded pdb=" CB SER C 155 " pdb=" CG2 THR C 303 " model vdw 2.243 3.860 nonbonded pdb=" NZ LYS C 213 " pdb=" O2' ADP C 401 " model vdw 2.265 3.120 nonbonded pdb=" NZ LYS F 213 " pdb=" O2' ADP F 401 " model vdw 2.268 3.120 ... (remaining 121786 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.520 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.860 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.012 0.087 14950 Z= 0.497 Angle : 0.815 8.430 20290 Z= 0.438 Chirality : 0.057 0.215 2255 Planarity : 0.005 0.056 2595 Dihedral : 13.665 89.369 5565 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.18), residues: 1845 helix: -1.36 (0.17), residues: 695 sheet: -1.50 (0.25), residues: 345 loop : -1.42 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP D 340 HIS 0.008 0.002 HIS D 275 PHE 0.021 0.002 PHE C 375 TYR 0.013 0.002 TYR D 143 ARG 0.005 0.001 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.17540 ( 698) hydrogen bonds : angle 6.18499 ( 1752) covalent geometry : bond 0.01187 (14950) covalent geometry : angle 0.81508 (20290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 ASP cc_start: 0.7216 (t0) cc_final: 0.6657 (p0) REVERT: C 81 ASP cc_start: 0.7778 (p0) cc_final: 0.7501 (p0) REVERT: C 190 MET cc_start: 0.8177 (mtp) cc_final: 0.7841 (mtm) REVERT: C 303 THR cc_start: 0.8495 (t) cc_final: 0.7994 (t) REVERT: D 236 LEU cc_start: 0.8386 (mt) cc_final: 0.7961 (mm) REVERT: E 82 MET cc_start: 0.7386 (tpp) cc_final: 0.7099 (tpp) REVERT: E 157 ASP cc_start: 0.7415 (t0) cc_final: 0.6903 (t70) REVERT: E 305 MET cc_start: 0.8342 (mmm) cc_final: 0.8127 (mmt) REVERT: F 34 ILE cc_start: 0.9257 (mt) cc_final: 0.9045 (tp) REVERT: F 67 LEU cc_start: 0.8874 (mt) cc_final: 0.8643 (mt) REVERT: F 330 ILE cc_start: 0.8999 (mp) cc_final: 0.8794 (mm) REVERT: F 346 LEU cc_start: 0.9306 (tp) cc_final: 0.9087 (tt) REVERT: A 190 MET cc_start: 0.7694 (mtp) cc_final: 0.7441 (mtm) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2624 time to fit residues: 169.2908 Evaluate side-chains 231 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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: 6.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 121 GLN C 275 HIS C 280 ASN C 297 ASN C 353 GLN D 87 HIS D 88 HIS D 92 ASN D 353 GLN E 40 HIS E 92 ASN E 353 GLN F 353 GLN A 73 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 162 ASN A 173 HIS A 297 ASN A 353 GLN A 371 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.046720 restraints weight = 61037.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.048474 restraints weight = 33173.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.049678 restraints weight = 21652.258| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14950 Z= 0.177 Angle : 0.654 8.216 20290 Z= 0.328 Chirality : 0.046 0.163 2255 Planarity : 0.005 0.037 2595 Dihedral : 6.010 49.873 2080 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % 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: -0.52 (0.20), residues: 1845 helix: 0.11 (0.20), residues: 725 sheet: -0.90 (0.28), residues: 345 loop : -0.30 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.015 0.002 HIS D 73 PHE 0.033 0.001 PHE D 262 TYR 0.014 0.001 TYR A 91 ARG 0.004 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 698) hydrogen bonds : angle 4.76871 ( 1752) covalent geometry : bond 0.00385 (14950) covalent geometry : angle 0.65379 (20290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 ASP cc_start: 0.8977 (t0) cc_final: 0.8760 (t0) REVERT: C 47 MET cc_start: 0.3211 (ttm) cc_final: 0.2602 (ttm) REVERT: C 81 ASP cc_start: 0.9084 (p0) cc_final: 0.8865 (p0) REVERT: C 154 ASP cc_start: 0.8074 (t0) cc_final: 0.7812 (t0) REVERT: C 205 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: C 246 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8082 (tp-100) REVERT: D 56 ASP cc_start: 0.9054 (t0) cc_final: 0.8748 (p0) REVERT: D 81 ASP cc_start: 0.9194 (m-30) cc_final: 0.8983 (m-30) REVERT: D 82 MET cc_start: 0.9228 (tpt) cc_final: 0.8901 (tpt) REVERT: D 107 GLU cc_start: 0.8884 (pt0) cc_final: 0.8593 (pt0) REVERT: D 179 ASP cc_start: 0.8695 (p0) cc_final: 0.8259 (t70) REVERT: D 184 ASP cc_start: 0.8976 (m-30) cc_final: 0.8732 (m-30) REVERT: D 205 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8595 (mt-10) REVERT: D 217 CYS cc_start: 0.9000 (m) cc_final: 0.8622 (m) REVERT: D 226 GLU cc_start: 0.9136 (tp30) cc_final: 0.8830 (tp30) REVERT: D 238 LYS cc_start: 0.9267 (mmtt) cc_final: 0.9058 (mmmm) REVERT: D 283 MET cc_start: 0.8749 (mmm) cc_final: 0.8466 (mmm) REVERT: D 355 MET cc_start: 0.8574 (mtp) cc_final: 0.8339 (mtp) REVERT: E 95 ARG cc_start: 0.9103 (mtt90) cc_final: 0.8727 (mpp80) REVERT: E 121 GLN cc_start: 0.9417 (tt0) cc_final: 0.8988 (tp40) REVERT: E 128 ASN cc_start: 0.9202 (t0) cc_final: 0.8916 (t0) REVERT: E 137 GLN cc_start: 0.9170 (mt0) cc_final: 0.8781 (mp10) REVERT: E 157 ASP cc_start: 0.8175 (t0) cc_final: 0.7903 (t70) REVERT: E 179 ASP cc_start: 0.7964 (p0) cc_final: 0.7531 (t0) REVERT: E 205 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8493 (mt-10) REVERT: E 217 CYS cc_start: 0.8647 (m) cc_final: 0.8257 (m) REVERT: E 244 ASP cc_start: 0.7670 (t70) cc_final: 0.7428 (t0) REVERT: E 313 MET cc_start: 0.9210 (tpp) cc_final: 0.9001 (tpp) REVERT: F 82 MET cc_start: 0.9397 (tpt) cc_final: 0.9058 (tpt) REVERT: F 205 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8360 (mt-10) REVERT: F 248 ILE cc_start: 0.9574 (pt) cc_final: 0.9223 (mt) REVERT: F 285 CYS cc_start: 0.9043 (m) cc_final: 0.8719 (m) REVERT: F 286 ASP cc_start: 0.8691 (t0) cc_final: 0.8383 (t0) REVERT: A 11 ASP cc_start: 0.8860 (t0) cc_final: 0.6659 (p0) REVERT: A 34 ILE cc_start: 0.8665 (tp) cc_final: 0.8374 (tp) REVERT: A 44 MET cc_start: 0.4841 (pmm) cc_final: 0.4598 (pmm) REVERT: A 103 THR cc_start: 0.9289 (m) cc_final: 0.8970 (m) REVERT: A 119 MET cc_start: 0.8868 (ptm) cc_final: 0.8263 (ptp) REVERT: A 179 ASP cc_start: 0.7808 (p0) cc_final: 0.7229 (t70) REVERT: A 227 MET cc_start: 0.8877 (mmm) cc_final: 0.8662 (mmm) REVERT: A 325 MET cc_start: 0.8405 (mmm) cc_final: 0.8167 (mmt) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.2331 time to fit residues: 101.0448 Evaluate side-chains 190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 173 HIS D 225 ASN E 87 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN F 225 ASN F 275 HIS F 371 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.043305 restraints weight = 63032.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.044848 restraints weight = 35684.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.045891 restraints weight = 23899.759| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14950 Z= 0.305 Angle : 0.758 9.314 20290 Z= 0.381 Chirality : 0.048 0.178 2255 Planarity : 0.005 0.037 2595 Dihedral : 6.046 58.324 2080 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1845 helix: 0.31 (0.20), residues: 725 sheet: -0.56 (0.30), residues: 310 loop : 0.18 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 79 HIS 0.015 0.002 HIS D 73 PHE 0.021 0.002 PHE F 124 TYR 0.022 0.002 TYR A 143 ARG 0.005 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 698) hydrogen bonds : angle 4.86212 ( 1752) covalent geometry : bond 0.00655 (14950) covalent geometry : angle 0.75815 (20290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6031 (ttt) cc_final: 0.5559 (ttm) REVERT: C 119 MET cc_start: 0.9137 (ttt) cc_final: 0.8901 (ttp) REVERT: C 154 ASP cc_start: 0.8397 (t0) cc_final: 0.8184 (t0) REVERT: C 205 GLU cc_start: 0.8735 (mp0) cc_final: 0.8497 (pm20) REVERT: C 285 CYS cc_start: 0.9199 (m) cc_final: 0.8946 (m) REVERT: D 82 MET cc_start: 0.9260 (tpt) cc_final: 0.8775 (tpp) REVERT: D 107 GLU cc_start: 0.9013 (pt0) cc_final: 0.8606 (pt0) REVERT: D 179 ASP cc_start: 0.8701 (p0) cc_final: 0.8345 (t0) REVERT: D 313 MET cc_start: 0.9205 (tpp) cc_final: 0.8805 (tpp) REVERT: D 355 MET cc_start: 0.8709 (mtp) cc_final: 0.8482 (mtp) REVERT: D 372 ARG cc_start: 0.9380 (mmm-85) cc_final: 0.9125 (mmm-85) REVERT: E 12 ASN cc_start: 0.9345 (p0) cc_final: 0.9126 (p0) REVERT: E 81 ASP cc_start: 0.8892 (t70) cc_final: 0.8335 (t70) REVERT: E 128 ASN cc_start: 0.9276 (t0) cc_final: 0.8959 (t0) REVERT: E 179 ASP cc_start: 0.8301 (p0) cc_final: 0.7613 (t0) REVERT: E 205 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8468 (mt-10) REVERT: E 244 ASP cc_start: 0.7570 (t70) cc_final: 0.7299 (t0) REVERT: E 313 MET cc_start: 0.9374 (tpp) cc_final: 0.9124 (tpp) REVERT: E 362 TYR cc_start: 0.9018 (t80) cc_final: 0.8627 (t80) REVERT: F 205 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8470 (mt-10) REVERT: F 225 ASN cc_start: 0.9204 (m-40) cc_final: 0.8989 (m-40) REVERT: F 285 CYS cc_start: 0.9067 (m) cc_final: 0.8770 (m) REVERT: F 286 ASP cc_start: 0.8925 (t0) cc_final: 0.8676 (t70) REVERT: F 355 MET cc_start: 0.8623 (mtm) cc_final: 0.8376 (ttm) REVERT: F 375 PHE cc_start: 0.7610 (t80) cc_final: 0.6898 (t80) REVERT: A 11 ASP cc_start: 0.9032 (t0) cc_final: 0.6702 (p0) REVERT: A 47 MET cc_start: 0.6889 (tpt) cc_final: 0.6406 (ttm) REVERT: A 59 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8112 (mm-40) REVERT: A 95 ARG cc_start: 0.9247 (pmt170) cc_final: 0.9026 (mtm-85) REVERT: A 105 LEU cc_start: 0.9354 (mt) cc_final: 0.8943 (mt) REVERT: A 132 MET cc_start: 0.9418 (ppp) cc_final: 0.8807 (ppp) REVERT: A 176 MET cc_start: 0.9539 (mmm) cc_final: 0.8929 (mpp) REVERT: A 227 MET cc_start: 0.8807 (mmm) cc_final: 0.8577 (mmm) REVERT: A 246 GLN cc_start: 0.8237 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 314 GLN cc_start: 0.9450 (tt0) cc_final: 0.9198 (tm-30) REVERT: A 325 MET cc_start: 0.8310 (mmm) cc_final: 0.8018 (mmt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2354 time to fit residues: 70.9840 Evaluate side-chains 155 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.056532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.043242 restraints weight = 63929.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.044773 restraints weight = 36792.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.045865 restraints weight = 25079.543| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14950 Z= 0.204 Angle : 0.653 9.085 20290 Z= 0.322 Chirality : 0.046 0.167 2255 Planarity : 0.004 0.037 2595 Dihedral : 5.822 52.656 2080 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1845 helix: 0.62 (0.20), residues: 725 sheet: -0.27 (0.31), residues: 320 loop : 0.36 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 79 HIS 0.010 0.001 HIS D 73 PHE 0.018 0.002 PHE A 124 TYR 0.014 0.001 TYR C 143 ARG 0.004 0.000 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 698) hydrogen bonds : angle 4.61483 ( 1752) covalent geometry : bond 0.00441 (14950) covalent geometry : angle 0.65256 (20290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLN cc_start: 0.8662 (tp40) cc_final: 0.8442 (tp40) REVERT: C 47 MET cc_start: 0.5991 (ttt) cc_final: 0.5630 (ttm) REVERT: C 154 ASP cc_start: 0.8015 (t0) cc_final: 0.7747 (t0) REVERT: C 176 MET cc_start: 0.9068 (tpp) cc_final: 0.8804 (mmm) REVERT: C 205 GLU cc_start: 0.8701 (mp0) cc_final: 0.8444 (pm20) REVERT: D 44 MET cc_start: 0.8839 (mmm) cc_final: 0.8621 (mmm) REVERT: D 82 MET cc_start: 0.9248 (tpt) cc_final: 0.8899 (tpt) REVERT: D 107 GLU cc_start: 0.8823 (pt0) cc_final: 0.8542 (pt0) REVERT: D 117 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8791 (mm-30) REVERT: D 179 ASP cc_start: 0.8618 (p0) cc_final: 0.8390 (t0) REVERT: D 205 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8456 (mt-10) REVERT: D 248 ILE cc_start: 0.9464 (pt) cc_final: 0.9213 (mt) REVERT: D 257 CYS cc_start: 0.9313 (t) cc_final: 0.9068 (t) REVERT: D 276 GLU cc_start: 0.9114 (tt0) cc_final: 0.8895 (tp30) REVERT: D 313 MET cc_start: 0.9082 (tpp) cc_final: 0.8732 (tpp) REVERT: D 326 LYS cc_start: 0.8598 (tptp) cc_final: 0.8220 (tptp) REVERT: D 355 MET cc_start: 0.8686 (mtp) cc_final: 0.8475 (mtp) REVERT: E 12 ASN cc_start: 0.9298 (p0) cc_final: 0.9079 (p0) REVERT: E 128 ASN cc_start: 0.9111 (t0) cc_final: 0.8796 (t0) REVERT: E 154 ASP cc_start: 0.8262 (t0) cc_final: 0.8047 (t0) REVERT: E 179 ASP cc_start: 0.8253 (p0) cc_final: 0.7602 (t0) REVERT: E 205 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8365 (mt-10) REVERT: E 244 ASP cc_start: 0.7369 (t70) cc_final: 0.7056 (t0) REVERT: E 283 MET cc_start: 0.8917 (tpp) cc_final: 0.8692 (mmm) REVERT: E 318 THR cc_start: 0.9413 (m) cc_final: 0.9213 (p) REVERT: E 362 TYR cc_start: 0.8898 (t80) cc_final: 0.8565 (t80) REVERT: F 44 MET cc_start: 0.8954 (mmm) cc_final: 0.8682 (mmm) REVERT: F 82 MET cc_start: 0.9091 (tpt) cc_final: 0.8830 (tpp) REVERT: F 205 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8380 (mt-10) REVERT: F 283 MET cc_start: 0.9016 (tpp) cc_final: 0.8807 (mmm) REVERT: F 285 CYS cc_start: 0.8942 (m) cc_final: 0.8658 (m) REVERT: F 355 MET cc_start: 0.8401 (mtm) cc_final: 0.8161 (ttm) REVERT: A 11 ASP cc_start: 0.9091 (t0) cc_final: 0.8767 (t0) REVERT: A 25 ASP cc_start: 0.9231 (m-30) cc_final: 0.8940 (p0) REVERT: A 104 LEU cc_start: 0.9260 (tt) cc_final: 0.9052 (tp) REVERT: A 105 LEU cc_start: 0.9292 (mt) cc_final: 0.9003 (mt) REVERT: A 132 MET cc_start: 0.9373 (ppp) cc_final: 0.8946 (ppp) REVERT: A 176 MET cc_start: 0.9548 (mmm) cc_final: 0.9037 (mpp) REVERT: A 227 MET cc_start: 0.8789 (mmm) cc_final: 0.8479 (mmm) REVERT: A 314 GLN cc_start: 0.9484 (tt0) cc_final: 0.9159 (tm-30) REVERT: A 354 GLN cc_start: 0.8747 (mp10) cc_final: 0.8489 (mp10) REVERT: A 355 MET cc_start: 0.8728 (mmp) cc_final: 0.8045 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2305 time to fit residues: 69.5445 Evaluate side-chains 154 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.042922 restraints weight = 63836.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.044529 restraints weight = 36261.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.045671 restraints weight = 24390.042| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14950 Z= 0.185 Angle : 0.637 8.661 20290 Z= 0.312 Chirality : 0.045 0.163 2255 Planarity : 0.004 0.037 2595 Dihedral : 5.708 49.176 2080 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1845 helix: 0.83 (0.19), residues: 750 sheet: -0.19 (0.31), residues: 320 loop : 0.31 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 86 HIS 0.009 0.001 HIS D 73 PHE 0.024 0.001 PHE F 375 TYR 0.014 0.001 TYR C 143 ARG 0.003 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 698) hydrogen bonds : angle 4.56292 ( 1752) covalent geometry : bond 0.00407 (14950) covalent geometry : angle 0.63660 (20290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6130 (ttt) cc_final: 0.5500 (ttm) REVERT: C 154 ASP cc_start: 0.8017 (t0) cc_final: 0.7669 (t0) REVERT: C 176 MET cc_start: 0.9136 (tpp) cc_final: 0.8850 (mmm) REVERT: C 205 GLU cc_start: 0.8725 (mp0) cc_final: 0.8431 (mp0) REVERT: D 44 MET cc_start: 0.8858 (mmm) cc_final: 0.8603 (mmm) REVERT: D 82 MET cc_start: 0.9219 (tpt) cc_final: 0.8815 (tpp) REVERT: D 107 GLU cc_start: 0.8786 (pt0) cc_final: 0.8482 (pt0) REVERT: D 179 ASP cc_start: 0.8694 (p0) cc_final: 0.8338 (t0) REVERT: D 205 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8450 (mt-10) REVERT: D 226 GLU cc_start: 0.9302 (tp30) cc_final: 0.8771 (tp30) REVERT: D 248 ILE cc_start: 0.9473 (pt) cc_final: 0.9201 (mt) REVERT: D 257 CYS cc_start: 0.9327 (t) cc_final: 0.9117 (t) REVERT: D 276 GLU cc_start: 0.9167 (tt0) cc_final: 0.8904 (tp30) REVERT: D 313 MET cc_start: 0.9088 (tpp) cc_final: 0.8747 (tpp) REVERT: D 325 MET cc_start: 0.8159 (tpp) cc_final: 0.7563 (tmm) REVERT: D 330 ILE cc_start: 0.9095 (tt) cc_final: 0.8841 (pt) REVERT: E 81 ASP cc_start: 0.8819 (t70) cc_final: 0.8314 (t70) REVERT: E 128 ASN cc_start: 0.9172 (t0) cc_final: 0.8843 (t0) REVERT: E 154 ASP cc_start: 0.8395 (t0) cc_final: 0.8154 (t0) REVERT: E 176 MET cc_start: 0.9018 (tpp) cc_final: 0.8784 (mmm) REVERT: E 179 ASP cc_start: 0.8331 (p0) cc_final: 0.7652 (t0) REVERT: E 205 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8334 (mt-10) REVERT: E 244 ASP cc_start: 0.7335 (t70) cc_final: 0.7054 (t0) REVERT: E 269 MET cc_start: 0.8590 (tpp) cc_final: 0.8246 (tmm) REVERT: E 270 GLU cc_start: 0.8445 (tp30) cc_final: 0.8217 (tt0) REVERT: E 283 MET cc_start: 0.9002 (tpp) cc_final: 0.8728 (mmm) REVERT: E 318 THR cc_start: 0.9391 (m) cc_final: 0.9168 (p) REVERT: E 355 MET cc_start: 0.8872 (mtp) cc_final: 0.8637 (mtp) REVERT: E 362 TYR cc_start: 0.8954 (t80) cc_final: 0.8617 (t80) REVERT: F 123 MET cc_start: 0.9154 (tpp) cc_final: 0.8946 (tpp) REVERT: F 132 MET cc_start: 0.9433 (tmm) cc_final: 0.9200 (tmm) REVERT: F 176 MET cc_start: 0.8938 (tpp) cc_final: 0.8617 (tpp) REVERT: F 283 MET cc_start: 0.9079 (tpp) cc_final: 0.8786 (mmm) REVERT: F 285 CYS cc_start: 0.8988 (m) cc_final: 0.8682 (m) REVERT: F 305 MET cc_start: 0.9121 (mmt) cc_final: 0.8563 (mmt) REVERT: F 355 MET cc_start: 0.8539 (mtm) cc_final: 0.8309 (ttm) REVERT: A 25 ASP cc_start: 0.9287 (m-30) cc_final: 0.9015 (p0) REVERT: A 59 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8283 (mm-40) REVERT: A 132 MET cc_start: 0.9410 (ppp) cc_final: 0.9169 (ppp) REVERT: A 176 MET cc_start: 0.9567 (mmm) cc_final: 0.8962 (mpp) REVERT: A 227 MET cc_start: 0.8776 (mmm) cc_final: 0.8490 (mmm) REVERT: A 314 GLN cc_start: 0.9487 (tt0) cc_final: 0.9167 (tm-30) REVERT: A 354 GLN cc_start: 0.8822 (mp10) cc_final: 0.8570 (mp10) REVERT: A 355 MET cc_start: 0.8761 (mmp) cc_final: 0.8081 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2447 time to fit residues: 74.9139 Evaluate side-chains 150 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 173 optimal weight: 0.0870 chunk 66 optimal weight: 20.0000 chunk 134 optimal weight: 0.0010 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.056693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.043179 restraints weight = 62737.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.044842 restraints weight = 35140.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.046029 restraints weight = 23347.202| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14950 Z= 0.143 Angle : 0.593 6.397 20290 Z= 0.290 Chirality : 0.045 0.159 2255 Planarity : 0.004 0.035 2595 Dihedral : 5.554 47.873 2080 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.75 (0.20), residues: 1845 helix: 1.03 (0.20), residues: 745 sheet: -0.06 (0.31), residues: 310 loop : 0.42 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 86 HIS 0.007 0.001 HIS D 73 PHE 0.020 0.001 PHE A 124 TYR 0.013 0.001 TYR A 91 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 698) hydrogen bonds : angle 4.44229 ( 1752) covalent geometry : bond 0.00319 (14950) covalent geometry : angle 0.59307 (20290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 CYS cc_start: 0.8375 (p) cc_final: 0.8154 (p) REVERT: C 47 MET cc_start: 0.6109 (ttt) cc_final: 0.5412 (ttm) REVERT: C 154 ASP cc_start: 0.8041 (t0) cc_final: 0.7734 (t0) REVERT: C 176 MET cc_start: 0.9194 (tpp) cc_final: 0.8898 (mmm) REVERT: C 205 GLU cc_start: 0.8754 (mp0) cc_final: 0.8409 (mp0) REVERT: C 227 MET cc_start: 0.9294 (mmp) cc_final: 0.8965 (mmm) REVERT: C 305 MET cc_start: 0.9509 (mtp) cc_final: 0.8864 (mtt) REVERT: D 82 MET cc_start: 0.9254 (tpt) cc_final: 0.8831 (tpt) REVERT: D 107 GLU cc_start: 0.8857 (pt0) cc_final: 0.8529 (pt0) REVERT: D 179 ASP cc_start: 0.8782 (p0) cc_final: 0.8356 (t0) REVERT: D 184 ASP cc_start: 0.9188 (m-30) cc_final: 0.8936 (m-30) REVERT: D 205 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8470 (mt-10) REVERT: D 226 GLU cc_start: 0.9328 (tp30) cc_final: 0.8737 (tp30) REVERT: D 276 GLU cc_start: 0.9186 (tt0) cc_final: 0.8954 (tp30) REVERT: D 313 MET cc_start: 0.9072 (tpp) cc_final: 0.8746 (tpp) REVERT: D 330 ILE cc_start: 0.9048 (tt) cc_final: 0.8795 (pt) REVERT: E 81 ASP cc_start: 0.8836 (t70) cc_final: 0.8303 (t70) REVERT: E 128 ASN cc_start: 0.9194 (t0) cc_final: 0.8865 (t0) REVERT: E 154 ASP cc_start: 0.8365 (t0) cc_final: 0.8047 (t0) REVERT: E 176 MET cc_start: 0.9073 (tpp) cc_final: 0.8837 (mmm) REVERT: E 179 ASP cc_start: 0.8296 (p0) cc_final: 0.7772 (t0) REVERT: E 205 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8355 (mt-10) REVERT: E 244 ASP cc_start: 0.7293 (t70) cc_final: 0.7013 (t0) REVERT: E 269 MET cc_start: 0.8716 (tpp) cc_final: 0.8411 (tmm) REVERT: E 270 GLU cc_start: 0.8472 (tp30) cc_final: 0.8205 (tt0) REVERT: E 313 MET cc_start: 0.9181 (tpp) cc_final: 0.8964 (tpp) REVERT: E 318 THR cc_start: 0.9366 (m) cc_final: 0.9150 (p) REVERT: E 355 MET cc_start: 0.8909 (mtp) cc_final: 0.8669 (mtp) REVERT: F 82 MET cc_start: 0.9196 (tpt) cc_final: 0.8921 (tpp) REVERT: F 176 MET cc_start: 0.9018 (tpp) cc_final: 0.8740 (tpp) REVERT: F 205 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8353 (mt-10) REVERT: F 283 MET cc_start: 0.9055 (tpp) cc_final: 0.8824 (mmm) REVERT: F 285 CYS cc_start: 0.8944 (m) cc_final: 0.8667 (m) REVERT: F 355 MET cc_start: 0.8626 (mtm) cc_final: 0.8404 (ttm) REVERT: A 25 ASP cc_start: 0.9285 (m-30) cc_final: 0.9010 (p0) REVERT: A 59 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8293 (mm-40) REVERT: A 132 MET cc_start: 0.9432 (ppp) cc_final: 0.9152 (ppp) REVERT: A 176 MET cc_start: 0.9533 (mmm) cc_final: 0.8877 (mpp) REVERT: A 227 MET cc_start: 0.8689 (mmm) cc_final: 0.8420 (mmm) REVERT: A 305 MET cc_start: 0.9125 (mmt) cc_final: 0.8805 (mmm) REVERT: A 314 GLN cc_start: 0.9478 (tt0) cc_final: 0.9167 (tm-30) REVERT: A 353 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8610 (mm-40) REVERT: A 354 GLN cc_start: 0.8838 (mp10) cc_final: 0.8588 (mp10) REVERT: A 355 MET cc_start: 0.8795 (mmp) cc_final: 0.8147 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2292 time to fit residues: 69.3737 Evaluate side-chains 153 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 0.0070 chunk 159 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.042943 restraints weight = 62937.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.044585 restraints weight = 35684.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.045758 restraints weight = 23704.051| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14950 Z= 0.154 Angle : 0.614 7.081 20290 Z= 0.298 Chirality : 0.045 0.177 2255 Planarity : 0.004 0.034 2595 Dihedral : 5.536 48.033 2080 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.87 (0.21), residues: 1845 helix: 1.04 (0.19), residues: 750 sheet: -0.05 (0.31), residues: 320 loop : 0.62 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.015 0.001 PHE A 124 TYR 0.011 0.001 TYR A 91 ARG 0.004 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 698) hydrogen bonds : angle 4.46194 ( 1752) covalent geometry : bond 0.00346 (14950) covalent geometry : angle 0.61379 (20290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: C 10 CYS cc_start: 0.8370 (p) cc_final: 0.8131 (p) REVERT: C 154 ASP cc_start: 0.8047 (t0) cc_final: 0.7741 (t0) REVERT: C 176 MET cc_start: 0.9188 (tpp) cc_final: 0.8890 (mmm) REVERT: C 205 GLU cc_start: 0.8885 (mp0) cc_final: 0.8600 (mp0) REVERT: D 82 MET cc_start: 0.9297 (tpt) cc_final: 0.8564 (tpp) REVERT: D 107 GLU cc_start: 0.8817 (pt0) cc_final: 0.8481 (pt0) REVERT: D 179 ASP cc_start: 0.8658 (p0) cc_final: 0.8361 (t0) REVERT: D 184 ASP cc_start: 0.9212 (m-30) cc_final: 0.8979 (m-30) REVERT: D 205 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8525 (mt-10) REVERT: D 226 GLU cc_start: 0.9319 (tp30) cc_final: 0.8683 (tp30) REVERT: D 276 GLU cc_start: 0.9160 (tt0) cc_final: 0.8943 (tp30) REVERT: D 313 MET cc_start: 0.9078 (tpp) cc_final: 0.8763 (tpp) REVERT: D 325 MET cc_start: 0.8362 (mmm) cc_final: 0.8028 (mmm) REVERT: D 330 ILE cc_start: 0.9049 (tt) cc_final: 0.8805 (pt) REVERT: E 81 ASP cc_start: 0.8819 (t70) cc_final: 0.8292 (t70) REVERT: E 128 ASN cc_start: 0.9197 (t0) cc_final: 0.8865 (t0) REVERT: E 154 ASP cc_start: 0.8335 (t0) cc_final: 0.8068 (t0) REVERT: E 176 MET cc_start: 0.9068 (tpp) cc_final: 0.8828 (mmm) REVERT: E 179 ASP cc_start: 0.8314 (p0) cc_final: 0.7733 (t0) REVERT: E 205 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8373 (mt-10) REVERT: E 244 ASP cc_start: 0.7326 (t70) cc_final: 0.7035 (t0) REVERT: E 269 MET cc_start: 0.8734 (tpp) cc_final: 0.8459 (tmm) REVERT: E 270 GLU cc_start: 0.8457 (tp30) cc_final: 0.8202 (tt0) REVERT: E 318 THR cc_start: 0.9367 (m) cc_final: 0.9143 (p) REVERT: F 82 MET cc_start: 0.9215 (tpt) cc_final: 0.8904 (tpp) REVERT: F 205 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8476 (mt-10) REVERT: F 270 GLU cc_start: 0.7842 (pm20) cc_final: 0.7576 (pm20) REVERT: F 283 MET cc_start: 0.9069 (tpp) cc_final: 0.8813 (mmm) REVERT: F 285 CYS cc_start: 0.8985 (m) cc_final: 0.8688 (m) REVERT: F 305 MET cc_start: 0.9005 (mmt) cc_final: 0.8394 (mmt) REVERT: F 375 PHE cc_start: 0.7666 (t80) cc_final: 0.7245 (m-10) REVERT: A 25 ASP cc_start: 0.9293 (m-30) cc_final: 0.9038 (p0) REVERT: A 59 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8316 (mm-40) REVERT: A 132 MET cc_start: 0.9424 (ppp) cc_final: 0.9144 (ppp) REVERT: A 176 MET cc_start: 0.9519 (mmm) cc_final: 0.8852 (mpp) REVERT: A 227 MET cc_start: 0.8689 (mmm) cc_final: 0.8410 (mmm) REVERT: A 314 GLN cc_start: 0.9483 (tt0) cc_final: 0.9165 (tm-30) REVERT: A 353 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8614 (mm-40) REVERT: A 354 GLN cc_start: 0.8869 (mp10) cc_final: 0.8632 (mp10) REVERT: A 355 MET cc_start: 0.8839 (mmp) cc_final: 0.8239 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2462 time to fit residues: 73.3233 Evaluate side-chains 152 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 15 optimal weight: 20.0000 chunk 95 optimal weight: 0.0570 chunk 120 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 173 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.043812 restraints weight = 62057.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.045450 restraints weight = 34926.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.046620 restraints weight = 23367.180| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14950 Z= 0.126 Angle : 0.606 7.822 20290 Z= 0.290 Chirality : 0.045 0.189 2255 Planarity : 0.004 0.034 2595 Dihedral : 5.434 52.268 2080 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.21), residues: 1845 helix: 1.31 (0.20), residues: 730 sheet: -0.01 (0.31), residues: 310 loop : 0.64 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 86 HIS 0.007 0.001 HIS D 73 PHE 0.016 0.001 PHE A 124 TYR 0.010 0.001 TYR A 143 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 698) hydrogen bonds : angle 4.39864 ( 1752) covalent geometry : bond 0.00286 (14950) covalent geometry : angle 0.60572 (20290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 CYS cc_start: 0.8390 (p) cc_final: 0.8151 (p) REVERT: C 78 ASN cc_start: 0.8968 (t0) cc_final: 0.8535 (t0) REVERT: C 107 GLU cc_start: 0.9040 (tt0) cc_final: 0.8812 (tt0) REVERT: C 154 ASP cc_start: 0.7945 (t0) cc_final: 0.7614 (t0) REVERT: C 176 MET cc_start: 0.9192 (tpp) cc_final: 0.8872 (mmm) REVERT: C 205 GLU cc_start: 0.8866 (mp0) cc_final: 0.8499 (mp0) REVERT: C 225 ASN cc_start: 0.9011 (m110) cc_final: 0.8808 (t0) REVERT: C 227 MET cc_start: 0.9158 (mmm) cc_final: 0.8772 (mmm) REVERT: C 252 ASN cc_start: 0.9473 (m-40) cc_final: 0.9127 (p0) REVERT: D 82 MET cc_start: 0.9156 (tpt) cc_final: 0.8737 (tpt) REVERT: D 107 GLU cc_start: 0.8781 (pt0) cc_final: 0.8439 (pt0) REVERT: D 179 ASP cc_start: 0.8724 (p0) cc_final: 0.8313 (t0) REVERT: D 184 ASP cc_start: 0.9178 (m-30) cc_final: 0.8957 (m-30) REVERT: D 276 GLU cc_start: 0.9141 (tt0) cc_final: 0.8911 (tp30) REVERT: D 313 MET cc_start: 0.9079 (tpp) cc_final: 0.8762 (tpp) REVERT: D 325 MET cc_start: 0.8285 (mmm) cc_final: 0.7580 (mmm) REVERT: D 330 ILE cc_start: 0.9054 (tt) cc_final: 0.8814 (pt) REVERT: E 128 ASN cc_start: 0.9125 (t0) cc_final: 0.8793 (t0) REVERT: E 154 ASP cc_start: 0.8305 (t0) cc_final: 0.7981 (t0) REVERT: E 176 MET cc_start: 0.9058 (tpp) cc_final: 0.8719 (mmm) REVERT: E 179 ASP cc_start: 0.8283 (p0) cc_final: 0.7760 (t0) REVERT: E 180 LEU cc_start: 0.9241 (tp) cc_final: 0.9010 (tp) REVERT: E 205 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8424 (mt-10) REVERT: E 227 MET cc_start: 0.9300 (mmp) cc_final: 0.9084 (mmm) REVERT: E 244 ASP cc_start: 0.7239 (t0) cc_final: 0.6973 (t0) REVERT: E 269 MET cc_start: 0.8714 (tpp) cc_final: 0.8465 (tmm) REVERT: E 270 GLU cc_start: 0.8432 (tp30) cc_final: 0.8187 (tt0) REVERT: E 318 THR cc_start: 0.9347 (m) cc_final: 0.9120 (p) REVERT: F 140 LEU cc_start: 0.9339 (mp) cc_final: 0.8970 (mp) REVERT: F 205 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8427 (mt-10) REVERT: F 270 GLU cc_start: 0.7752 (pm20) cc_final: 0.7519 (pm20) REVERT: F 285 CYS cc_start: 0.8925 (m) cc_final: 0.8658 (m) REVERT: F 305 MET cc_start: 0.9029 (mmt) cc_final: 0.8408 (mmt) REVERT: F 313 MET cc_start: 0.9186 (tpp) cc_final: 0.8896 (tpp) REVERT: A 25 ASP cc_start: 0.9270 (m-30) cc_final: 0.9021 (p0) REVERT: A 59 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 95 ARG cc_start: 0.9234 (pmt170) cc_final: 0.9025 (mpp80) REVERT: A 176 MET cc_start: 0.9511 (mmm) cc_final: 0.8834 (mpp) REVERT: A 217 CYS cc_start: 0.8165 (m) cc_final: 0.7960 (m) REVERT: A 227 MET cc_start: 0.8659 (mmm) cc_final: 0.8373 (mmm) REVERT: A 287 ILE cc_start: 0.9186 (tt) cc_final: 0.8963 (mt) REVERT: A 314 GLN cc_start: 0.9485 (tt0) cc_final: 0.9166 (tm-30) REVERT: A 353 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8625 (mm-40) REVERT: A 354 GLN cc_start: 0.8887 (mp10) cc_final: 0.8644 (mp10) REVERT: A 355 MET cc_start: 0.8849 (mmp) cc_final: 0.8272 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2159 time to fit residues: 68.1497 Evaluate side-chains 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.056510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.043148 restraints weight = 62541.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.044804 restraints weight = 35710.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.045921 restraints weight = 23552.148| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14950 Z= 0.174 Angle : 0.638 8.442 20290 Z= 0.309 Chirality : 0.045 0.180 2255 Planarity : 0.004 0.034 2595 Dihedral : 5.500 55.838 2080 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.87 (0.21), residues: 1845 helix: 1.02 (0.19), residues: 760 sheet: 0.07 (0.31), residues: 310 loop : 0.57 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 86 HIS 0.007 0.001 HIS D 73 PHE 0.014 0.001 PHE D 266 TYR 0.018 0.001 TYR E 143 ARG 0.004 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 698) hydrogen bonds : angle 4.47158 ( 1752) covalent geometry : bond 0.00386 (14950) covalent geometry : angle 0.63823 (20290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: C 10 CYS cc_start: 0.8452 (p) cc_final: 0.8178 (p) REVERT: C 78 ASN cc_start: 0.8962 (t0) cc_final: 0.8506 (t0) REVERT: C 154 ASP cc_start: 0.8099 (t0) cc_final: 0.7766 (t0) REVERT: C 176 MET cc_start: 0.9193 (tpp) cc_final: 0.8825 (mmm) REVERT: C 205 GLU cc_start: 0.8909 (mp0) cc_final: 0.8535 (mp0) REVERT: C 225 ASN cc_start: 0.8961 (m110) cc_final: 0.8753 (t0) REVERT: C 227 MET cc_start: 0.9178 (mmm) cc_final: 0.8797 (mmm) REVERT: C 252 ASN cc_start: 0.9462 (m-40) cc_final: 0.9158 (p0) REVERT: D 82 MET cc_start: 0.9180 (tpt) cc_final: 0.8930 (tpt) REVERT: D 107 GLU cc_start: 0.8779 (pt0) cc_final: 0.8465 (pt0) REVERT: D 179 ASP cc_start: 0.8681 (p0) cc_final: 0.8287 (t0) REVERT: D 184 ASP cc_start: 0.9191 (m-30) cc_final: 0.8954 (m-30) REVERT: D 276 GLU cc_start: 0.9155 (tt0) cc_final: 0.8921 (tp30) REVERT: D 313 MET cc_start: 0.9109 (tpp) cc_final: 0.8807 (tpp) REVERT: D 325 MET cc_start: 0.8284 (mmm) cc_final: 0.7708 (mmm) REVERT: D 330 ILE cc_start: 0.9085 (tt) cc_final: 0.8800 (pt) REVERT: E 47 MET cc_start: 0.6424 (ptp) cc_final: 0.5942 (ptp) REVERT: E 121 GLN cc_start: 0.9438 (tt0) cc_final: 0.9134 (tm-30) REVERT: E 128 ASN cc_start: 0.9136 (t0) cc_final: 0.8779 (t0) REVERT: E 154 ASP cc_start: 0.8504 (t0) cc_final: 0.8249 (t0) REVERT: E 176 MET cc_start: 0.9066 (tpp) cc_final: 0.8747 (mmm) REVERT: E 179 ASP cc_start: 0.8432 (p0) cc_final: 0.7590 (t0) REVERT: E 205 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8441 (mt-10) REVERT: E 244 ASP cc_start: 0.7305 (t0) cc_final: 0.7016 (t0) REVERT: E 318 THR cc_start: 0.9386 (m) cc_final: 0.9136 (p) REVERT: E 353 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8726 (mm-40) REVERT: F 176 MET cc_start: 0.8980 (tpp) cc_final: 0.8681 (tpp) REVERT: F 205 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 285 CYS cc_start: 0.8969 (m) cc_final: 0.8669 (m) REVERT: F 305 MET cc_start: 0.9078 (mmt) cc_final: 0.8462 (mmt) REVERT: F 313 MET cc_start: 0.9246 (tpp) cc_final: 0.8962 (tpp) REVERT: A 59 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8282 (mm-40) REVERT: A 95 ARG cc_start: 0.9239 (pmt170) cc_final: 0.9018 (mpp80) REVERT: A 132 MET cc_start: 0.9375 (ppp) cc_final: 0.9163 (ppp) REVERT: A 176 MET cc_start: 0.9495 (mmm) cc_final: 0.8804 (mpp) REVERT: A 227 MET cc_start: 0.8685 (mmm) cc_final: 0.8414 (mmm) REVERT: A 287 ILE cc_start: 0.9224 (tt) cc_final: 0.8973 (mt) REVERT: A 314 GLN cc_start: 0.9487 (tt0) cc_final: 0.9165 (tm-30) REVERT: A 353 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8710 (mm-40) REVERT: A 354 GLN cc_start: 0.8903 (mp10) cc_final: 0.8675 (mp10) REVERT: A 355 MET cc_start: 0.8858 (mmp) cc_final: 0.8347 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2221 time to fit residues: 70.0074 Evaluate side-chains 153 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 75 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 60 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.043359 restraints weight = 62300.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.045031 restraints weight = 35211.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.046166 restraints weight = 23147.399| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14950 Z= 0.156 Angle : 0.639 8.673 20290 Z= 0.306 Chirality : 0.045 0.180 2255 Planarity : 0.004 0.034 2595 Dihedral : 5.485 58.287 2080 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.87 (0.21), residues: 1845 helix: 0.99 (0.19), residues: 760 sheet: -0.07 (0.30), residues: 335 loop : 0.69 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 86 HIS 0.007 0.001 HIS D 73 PHE 0.012 0.001 PHE D 266 TYR 0.014 0.001 TYR E 143 ARG 0.005 0.000 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 698) hydrogen bonds : angle 4.44936 ( 1752) covalent geometry : bond 0.00350 (14950) covalent geometry : angle 0.63928 (20290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 CYS cc_start: 0.8537 (p) cc_final: 0.8249 (p) REVERT: C 78 ASN cc_start: 0.8953 (t0) cc_final: 0.8485 (t0) REVERT: C 154 ASP cc_start: 0.8044 (t0) cc_final: 0.7716 (t0) REVERT: C 176 MET cc_start: 0.9211 (tpp) cc_final: 0.8833 (mmm) REVERT: C 205 GLU cc_start: 0.8913 (mp0) cc_final: 0.8539 (mp0) REVERT: C 225 ASN cc_start: 0.8981 (m110) cc_final: 0.8749 (t0) REVERT: C 227 MET cc_start: 0.9180 (mmm) cc_final: 0.8791 (mmm) REVERT: C 252 ASN cc_start: 0.9449 (m-40) cc_final: 0.9129 (p0) REVERT: C 285 CYS cc_start: 0.9246 (m) cc_final: 0.9021 (m) REVERT: C 305 MET cc_start: 0.9442 (mtp) cc_final: 0.8941 (mtt) REVERT: D 82 MET cc_start: 0.9210 (tpt) cc_final: 0.8938 (tpt) REVERT: D 107 GLU cc_start: 0.8763 (pt0) cc_final: 0.8459 (pt0) REVERT: D 179 ASP cc_start: 0.8814 (p0) cc_final: 0.8261 (t0) REVERT: D 184 ASP cc_start: 0.9205 (m-30) cc_final: 0.8971 (m-30) REVERT: D 257 CYS cc_start: 0.9261 (t) cc_final: 0.9045 (t) REVERT: D 276 GLU cc_start: 0.9164 (tt0) cc_final: 0.8920 (tp30) REVERT: D 313 MET cc_start: 0.9112 (tpp) cc_final: 0.8805 (tpp) REVERT: D 325 MET cc_start: 0.8256 (mmm) cc_final: 0.7674 (mmm) REVERT: D 330 ILE cc_start: 0.9062 (tt) cc_final: 0.8771 (pt) REVERT: D 355 MET cc_start: 0.8873 (mtp) cc_final: 0.8660 (mtp) REVERT: E 47 MET cc_start: 0.6471 (ptp) cc_final: 0.6077 (ptp) REVERT: E 121 GLN cc_start: 0.9449 (tt0) cc_final: 0.9134 (tm-30) REVERT: E 128 ASN cc_start: 0.9132 (t0) cc_final: 0.8800 (t0) REVERT: E 154 ASP cc_start: 0.8487 (t0) cc_final: 0.8204 (t0) REVERT: E 176 MET cc_start: 0.9085 (tpp) cc_final: 0.8735 (mmm) REVERT: E 179 ASP cc_start: 0.8421 (p0) cc_final: 0.7557 (t0) REVERT: E 205 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8414 (mt-10) REVERT: E 227 MET cc_start: 0.9357 (mmp) cc_final: 0.9124 (mmm) REVERT: E 244 ASP cc_start: 0.7363 (t0) cc_final: 0.7043 (t0) REVERT: E 270 GLU cc_start: 0.8386 (tt0) cc_final: 0.7968 (tm-30) REVERT: E 318 THR cc_start: 0.9394 (m) cc_final: 0.9138 (p) REVERT: E 353 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8666 (mm-40) REVERT: F 82 MET cc_start: 0.9106 (tpt) cc_final: 0.8756 (tpt) REVERT: F 176 MET cc_start: 0.9002 (tpp) cc_final: 0.8687 (tpp) REVERT: F 285 CYS cc_start: 0.8968 (m) cc_final: 0.8690 (m) REVERT: F 305 MET cc_start: 0.9102 (mmt) cc_final: 0.8486 (mmt) REVERT: F 313 MET cc_start: 0.9236 (tpp) cc_final: 0.8952 (tpp) REVERT: A 59 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8295 (mm-40) REVERT: A 95 ARG cc_start: 0.9250 (pmt170) cc_final: 0.9019 (mpp80) REVERT: A 176 MET cc_start: 0.9467 (mmm) cc_final: 0.8761 (mpp) REVERT: A 184 ASP cc_start: 0.9243 (m-30) cc_final: 0.9036 (m-30) REVERT: A 227 MET cc_start: 0.8643 (mmm) cc_final: 0.8343 (mmm) REVERT: A 287 ILE cc_start: 0.9167 (tt) cc_final: 0.8950 (mt) REVERT: A 314 GLN cc_start: 0.9483 (tt0) cc_final: 0.9160 (tm-30) REVERT: A 353 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8709 (mm-40) REVERT: A 354 GLN cc_start: 0.8929 (mp10) cc_final: 0.8686 (mp10) REVERT: A 355 MET cc_start: 0.8882 (mmp) cc_final: 0.8356 (mmm) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2070 time to fit residues: 65.1790 Evaluate side-chains 153 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 157 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.045169 restraints weight = 60986.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.046887 restraints weight = 34357.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.048066 restraints weight = 22677.879| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14950 Z= 0.099 Angle : 0.622 8.824 20290 Z= 0.292 Chirality : 0.045 0.169 2255 Planarity : 0.004 0.034 2595 Dihedral : 5.260 56.324 2080 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.14 (0.21), residues: 1845 helix: 1.38 (0.20), residues: 720 sheet: 0.05 (0.30), residues: 325 loop : 0.69 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 86 HIS 0.005 0.001 HIS D 73 PHE 0.009 0.001 PHE F 124 TYR 0.019 0.001 TYR C 143 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 698) hydrogen bonds : angle 4.33071 ( 1752) covalent geometry : bond 0.00222 (14950) covalent geometry : angle 0.62247 (20290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.57 seconds wall clock time: 69 minutes 11.60 seconds (4151.60 seconds total)