Starting phenix.real_space_refine on Thu Jun 12 20:26:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zj1_60135/06_2025/8zj1_60135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zj1_60135/06_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_60135/06_2025/8zj1_60135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zj1_60135/06_2025/8zj1_60135.map" model { file = "/net/cci-nas-00/data/ceres_data/8zj1_60135/06_2025/8zj1_60135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zj1_60135/06_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-5710/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: 9.35, per 1000 atoms: 0.64 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 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: 1.84 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: 5.05 Time building geometry restraints manager: 4.14 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: 1.000 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.640 Find NCS groups from input model: 0.550 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- 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 : 1.613 Fit side-chains revert: symmetry clash 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: 0.6659 (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: 0.7844 (mtm) REVERT: C 303 THR cc_start: 0.8495 (t) cc_final: 0.7970 (t) REVERT: D 236 LEU cc_start: 0.8386 (mt) cc_final: 0.7960 (mm) REVERT: E 82 MET cc_start: 0.7386 (tpp) cc_final: 0.7100 (tpp) REVERT: E 157 ASP cc_start: 0.7415 (t0) cc_final: 0.6883 (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: 0.7440 (mtm) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2583 time to fit residues: 166.6554 Evaluate side-chains 232 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 88 HIS D 92 ASN D 225 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 275 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 = 0.060211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.046554 restraints weight = 61049.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.048344 restraints weight = 33190.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.049578 restraints weight = 21509.064| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3218 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 : 0.655 8.040 20290 Z= 0.328 Chirality : 0.046 0.165 2255 Planarity : 0.005 0.036 2595 Dihedral : 6.101 54.355 2080 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % 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: -0.54 (0.20), residues: 1845 helix: 0.07 (0.20), residues: 725 sheet: -0.89 (0.28), residues: 345 loop : -0.31 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.020 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 0.03734 ( 698) hydrogen bonds : angle 4.78419 ( 1752) covalent geometry : bond 0.00376 (14950) covalent geometry : angle 0.65478 (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 286 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 1.760 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: 0.8963 (t0) cc_final: 0.8743 (t0) REVERT: C 47 MET cc_start: 0.3262 (ttm) cc_final: 0.2656 (ttm) REVERT: C 81 ASP cc_start: 0.9085 (p0) cc_final: 0.8853 (p0) REVERT: C 154 ASP cc_start: 0.8073 (t0) cc_final: 0.7823 (t0) REVERT: C 179 ASP cc_start: 0.7206 (t0) cc_final: 0.7004 (t0) REVERT: C 205 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: C 246 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8109 (tp-100) REVERT: D 56 ASP cc_start: 0.9076 (t0) cc_final: 0.8751 (p0) REVERT: D 81 ASP cc_start: 0.9211 (m-30) cc_final: 0.9001 (m-30) REVERT: D 82 MET cc_start: 0.9247 (tpt) cc_final: 0.8916 (tpt) REVERT: D 107 GLU cc_start: 0.8914 (pt0) cc_final: 0.8622 (pt0) REVERT: D 179 ASP cc_start: 0.8717 (p0) cc_final: 0.8272 (t70) REVERT: D 184 ASP cc_start: 0.8971 (m-30) cc_final: 0.8717 (m-30) REVERT: D 205 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8605 (mt-10) REVERT: D 217 CYS cc_start: 0.9006 (m) cc_final: 0.8629 (m) REVERT: D 226 GLU cc_start: 0.9169 (tp30) cc_final: 0.8847 (tp30) REVERT: D 238 LYS cc_start: 0.9264 (mmtt) cc_final: 0.9058 (mmmm) REVERT: D 283 MET cc_start: 0.8740 (mmm) cc_final: 0.8483 (mmm) REVERT: D 355 MET cc_start: 0.8582 (mtp) cc_final: 0.8335 (mtp) REVERT: E 95 ARG cc_start: 0.9104 (mtt90) cc_final: 0.8722 (mpp80) REVERT: E 121 GLN cc_start: 0.9421 (tt0) cc_final: 0.8986 (tp40) REVERT: E 128 ASN cc_start: 0.9211 (t0) cc_final: 0.8913 (t0) REVERT: E 137 GLN cc_start: 0.9170 (mt0) cc_final: 0.8774 (mp10) REVERT: E 157 ASP cc_start: 0.8124 (t0) cc_final: 0.7867 (t70) REVERT: E 179 ASP cc_start: 0.7965 (p0) cc_final: 0.7459 (t0) REVERT: E 205 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8464 (mt-10) REVERT: E 217 CYS cc_start: 0.8654 (m) cc_final: 0.8292 (m) REVERT: E 244 ASP cc_start: 0.7722 (t70) cc_final: 0.7479 (t0) REVERT: E 313 MET cc_start: 0.9221 (tpp) cc_final: 0.8999 (tpp) REVERT: F 82 MET cc_start: 0.9418 (tpt) cc_final: 0.9081 (tpt) REVERT: F 205 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8360 (mt-10) REVERT: F 285 CYS cc_start: 0.9041 (m) cc_final: 0.8707 (m) REVERT: F 286 ASP cc_start: 0.8695 (t0) cc_final: 0.8384 (t0) REVERT: A 11 ASP cc_start: 0.8869 (t0) cc_final: 0.6688 (p0) REVERT: A 34 ILE cc_start: 0.8678 (tp) cc_final: 0.8391 (tp) REVERT: A 44 MET cc_start: 0.4897 (pmm) cc_final: 0.4643 (pmm) REVERT: A 103 THR cc_start: 0.9290 (m) cc_final: 0.8937 (m) REVERT: A 119 MET cc_start: 0.8855 (ptm) cc_final: 0.8416 (ptp) REVERT: A 179 ASP cc_start: 0.7802 (p0) cc_final: 0.7206 (t70) REVERT: A 227 MET cc_start: 0.8880 (mmm) cc_final: 0.8670 (mmm) REVERT: A 325 MET cc_start: 0.8373 (mmm) cc_final: 0.8161 (mmt) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.2483 time to fit residues: 106.9965 Evaluate side-chains 195 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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: 8.9990 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 E 353 GLN F 275 HIS F 371 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.057392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.043973 restraints weight = 62046.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.045604 restraints weight = 34523.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.046718 restraints weight = 22899.747| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14950 Z= 0.229 Angle : 0.680 10.187 20290 Z= 0.339 Chirality : 0.046 0.160 2255 Planarity : 0.005 0.040 2595 Dihedral : 5.813 53.717 2080 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: 0.07 (0.20), residues: 1845 helix: 0.43 (0.20), residues: 725 sheet: -0.51 (0.30), residues: 310 loop : 0.12 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.012 0.002 HIS E 371 PHE 0.016 0.002 PHE D 124 TYR 0.022 0.001 TYR A 143 ARG 0.005 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 698) hydrogen bonds : angle 4.64848 ( 1752) covalent geometry : bond 0.00500 (14950) covalent geometry : angle 0.68012 (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 216 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6051 (ttt) cc_final: 0.5650 (ttm) REVERT: C 119 MET cc_start: 0.9210 (ttt) cc_final: 0.8943 (ttm) REVERT: C 154 ASP cc_start: 0.8217 (t0) cc_final: 0.7955 (t0) REVERT: C 179 ASP cc_start: 0.7580 (t0) cc_final: 0.7307 (t0) REVERT: C 205 GLU cc_start: 0.8614 (mp0) cc_final: 0.8359 (pm20) REVERT: C 285 CYS cc_start: 0.9141 (m) cc_final: 0.8934 (m) REVERT: D 56 ASP cc_start: 0.9104 (t0) cc_final: 0.8890 (p0) REVERT: D 81 ASP cc_start: 0.9253 (m-30) cc_final: 0.9047 (m-30) REVERT: D 82 MET cc_start: 0.9235 (tpt) cc_final: 0.8524 (tpp) REVERT: D 107 GLU cc_start: 0.8980 (pt0) cc_final: 0.8621 (pt0) REVERT: D 179 ASP cc_start: 0.8675 (p0) cc_final: 0.8367 (t0) REVERT: D 205 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8467 (mt-10) REVERT: D 226 GLU cc_start: 0.9275 (tp30) cc_final: 0.8852 (tp30) REVERT: D 305 MET cc_start: 0.8949 (tpp) cc_final: 0.8451 (mmt) REVERT: D 313 MET cc_start: 0.9052 (tpp) cc_final: 0.8726 (tpp) REVERT: D 355 MET cc_start: 0.8667 (mtp) cc_final: 0.8442 (mtp) REVERT: D 372 ARG cc_start: 0.9285 (mmm-85) cc_final: 0.9054 (mmm-85) REVERT: E 12 ASN cc_start: 0.9317 (p0) cc_final: 0.9108 (p0) REVERT: E 81 ASP cc_start: 0.8885 (t70) cc_final: 0.8277 (t70) REVERT: E 128 ASN cc_start: 0.9224 (t0) cc_final: 0.8905 (t0) REVERT: E 154 ASP cc_start: 0.8675 (t0) cc_final: 0.8454 (t0) REVERT: E 179 ASP cc_start: 0.8196 (p0) cc_final: 0.7561 (t0) REVERT: E 180 LEU cc_start: 0.9270 (tp) cc_final: 0.9061 (tp) REVERT: E 205 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8420 (mt-10) REVERT: E 227 MET cc_start: 0.9287 (mmp) cc_final: 0.9040 (mmm) REVERT: E 244 ASP cc_start: 0.7557 (t70) cc_final: 0.7306 (t0) REVERT: E 305 MET cc_start: 0.9203 (mmp) cc_final: 0.8989 (mmp) REVERT: E 313 MET cc_start: 0.9346 (tpp) cc_final: 0.9116 (tpp) REVERT: E 362 TYR cc_start: 0.8987 (t80) cc_final: 0.8596 (t80) REVERT: F 285 CYS cc_start: 0.9030 (m) cc_final: 0.8729 (m) REVERT: F 286 ASP cc_start: 0.8819 (t0) cc_final: 0.8538 (t70) REVERT: F 313 MET cc_start: 0.9258 (ttm) cc_final: 0.9005 (tpp) REVERT: F 318 THR cc_start: 0.9328 (m) cc_final: 0.9103 (p) REVERT: F 375 PHE cc_start: 0.7471 (t80) cc_final: 0.6761 (t80) REVERT: A 11 ASP cc_start: 0.8988 (t0) cc_final: 0.6779 (p0) REVERT: A 47 MET cc_start: 0.6827 (tpt) cc_final: 0.6250 (ttm) REVERT: A 105 LEU cc_start: 0.9390 (mt) cc_final: 0.9112 (mp) REVERT: A 176 MET cc_start: 0.9550 (mmm) cc_final: 0.8941 (mpp) REVERT: A 227 MET cc_start: 0.8831 (mmm) cc_final: 0.8584 (mmm) REVERT: A 314 GLN cc_start: 0.9443 (tt0) cc_final: 0.9167 (tm-30) REVERT: A 325 MET cc_start: 0.8333 (mmm) cc_final: 0.8066 (mmt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2435 time to fit residues: 81.3675 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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: 10.0000 chunk 100 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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** F 225 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 161 HIS A 275 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.056408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.042972 restraints weight = 63934.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.044585 restraints weight = 37046.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.045654 restraints weight = 24717.934| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14950 Z= 0.243 Angle : 0.685 7.935 20290 Z= 0.342 Chirality : 0.047 0.169 2255 Planarity : 0.005 0.037 2595 Dihedral : 5.867 53.699 2080 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.16 (0.20), residues: 1845 helix: 0.48 (0.19), residues: 755 sheet: -0.49 (0.30), residues: 310 loop : 0.21 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 79 HIS 0.011 0.002 HIS D 73 PHE 0.015 0.002 PHE A 124 TYR 0.016 0.001 TYR C 143 ARG 0.005 0.000 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 698) hydrogen bonds : angle 4.64572 ( 1752) covalent geometry : bond 0.00525 (14950) covalent geometry : angle 0.68531 (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 205 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6088 (ttt) cc_final: 0.5524 (ttm) REVERT: C 154 ASP cc_start: 0.8260 (t0) cc_final: 0.7986 (t0) REVERT: C 205 GLU cc_start: 0.8693 (mp0) cc_final: 0.8418 (pm20) REVERT: C 285 CYS cc_start: 0.9130 (m) cc_final: 0.8926 (m) REVERT: D 81 ASP cc_start: 0.9231 (m-30) cc_final: 0.9024 (m-30) REVERT: D 82 MET cc_start: 0.9285 (tpt) cc_final: 0.8611 (tpp) REVERT: D 107 GLU cc_start: 0.8896 (pt0) cc_final: 0.8573 (pt0) REVERT: D 117 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8805 (mm-30) REVERT: D 179 ASP cc_start: 0.8699 (p0) cc_final: 0.8375 (t0) REVERT: D 205 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8445 (mt-10) REVERT: D 248 ILE cc_start: 0.9518 (pt) cc_final: 0.9222 (mt) REVERT: D 257 CYS cc_start: 0.9324 (t) cc_final: 0.9089 (t) REVERT: D 276 GLU cc_start: 0.9166 (tt0) cc_final: 0.8930 (tp30) REVERT: D 313 MET cc_start: 0.9053 (tpp) cc_final: 0.8679 (tpp) REVERT: D 355 MET cc_start: 0.8757 (mtp) cc_final: 0.8487 (mtp) REVERT: E 12 ASN cc_start: 0.9338 (p0) cc_final: 0.9117 (p0) REVERT: E 128 ASN cc_start: 0.9196 (t0) cc_final: 0.8883 (t0) REVERT: E 179 ASP cc_start: 0.8285 (p0) cc_final: 0.7605 (t0) REVERT: E 205 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8322 (mt-10) REVERT: E 244 ASP cc_start: 0.7435 (t70) cc_final: 0.7108 (t0) REVERT: E 313 MET cc_start: 0.9281 (tpp) cc_final: 0.9069 (tpp) REVERT: E 362 TYR cc_start: 0.8984 (t80) cc_final: 0.8645 (t80) REVERT: F 82 MET cc_start: 0.9194 (tpt) cc_final: 0.8973 (tpp) REVERT: F 107 GLU cc_start: 0.7620 (tt0) cc_final: 0.7281 (tt0) REVERT: F 123 MET cc_start: 0.9211 (tpp) cc_final: 0.8999 (tpp) REVERT: F 205 GLU cc_start: 0.8894 (mp0) cc_final: 0.8660 (pm20) REVERT: F 283 MET cc_start: 0.9083 (tpp) cc_final: 0.8845 (mmm) REVERT: F 285 CYS cc_start: 0.8977 (m) cc_final: 0.8684 (m) REVERT: A 11 ASP cc_start: 0.9047 (t0) cc_final: 0.6800 (p0) REVERT: A 47 MET cc_start: 0.7088 (tpt) cc_final: 0.6529 (ttm) REVERT: A 104 LEU cc_start: 0.9208 (tt) cc_final: 0.9000 (tp) REVERT: A 105 LEU cc_start: 0.9367 (mt) cc_final: 0.9123 (mt) REVERT: A 176 MET cc_start: 0.9552 (mmm) cc_final: 0.8997 (mpp) REVERT: A 227 MET cc_start: 0.8746 (mmm) cc_final: 0.8501 (mmm) REVERT: A 314 GLN cc_start: 0.9476 (tt0) cc_final: 0.9151 (tm-30) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2410 time to fit residues: 76.2905 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 : 1.741 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 128 ASN ** 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 = 0.2927 r_free = 0.2927 target = 0.056908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.043278 restraints weight = 63280.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.044911 restraints weight = 36175.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.046071 restraints weight = 24266.900| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14950 Z= 0.167 Angle : 0.633 8.835 20290 Z= 0.308 Chirality : 0.045 0.173 2255 Planarity : 0.004 0.037 2595 Dihedral : 5.677 49.182 2080 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1845 helix: 0.81 (0.19), residues: 755 sheet: -0.16 (0.30), residues: 320 loop : 0.32 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.026 0.001 PHE F 375 TYR 0.013 0.001 TYR A 91 ARG 0.007 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 698) hydrogen bonds : angle 4.46487 ( 1752) covalent geometry : bond 0.00367 (14950) covalent geometry : angle 0.63275 (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 207 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6161 (ttt) cc_final: 0.5498 (ttm) REVERT: C 154 ASP cc_start: 0.7990 (t0) cc_final: 0.7663 (t0) REVERT: C 205 GLU cc_start: 0.8720 (mp0) cc_final: 0.8370 (mp0) REVERT: D 82 MET cc_start: 0.9255 (tpt) cc_final: 0.8742 (tpp) REVERT: D 107 GLU cc_start: 0.8827 (pt0) cc_final: 0.8530 (pt0) REVERT: D 179 ASP cc_start: 0.8754 (p0) cc_final: 0.8400 (t0) REVERT: D 205 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 226 GLU cc_start: 0.9316 (tp30) cc_final: 0.8779 (tp30) REVERT: D 248 ILE cc_start: 0.9467 (pt) cc_final: 0.9172 (mt) REVERT: D 276 GLU cc_start: 0.9166 (tt0) cc_final: 0.8893 (tp30) REVERT: D 313 MET cc_start: 0.9041 (tpp) cc_final: 0.8703 (tpp) REVERT: D 330 ILE cc_start: 0.9112 (tt) cc_final: 0.8786 (pt) REVERT: D 355 MET cc_start: 0.8746 (mtp) cc_final: 0.8517 (mtp) REVERT: E 81 ASP cc_start: 0.8809 (t70) cc_final: 0.8297 (t70) REVERT: E 128 ASN cc_start: 0.9144 (t0) cc_final: 0.8798 (t0) REVERT: E 176 MET cc_start: 0.8996 (tpp) cc_final: 0.8764 (mmm) REVERT: E 179 ASP cc_start: 0.8347 (p0) cc_final: 0.7617 (t0) REVERT: E 180 LEU cc_start: 0.9261 (tp) cc_final: 0.9039 (tp) REVERT: E 205 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8319 (mt-10) REVERT: E 244 ASP cc_start: 0.7301 (t70) cc_final: 0.7033 (t0) REVERT: E 305 MET cc_start: 0.8733 (mmp) cc_final: 0.8496 (mmp) REVERT: E 313 MET cc_start: 0.9181 (tpp) cc_final: 0.8972 (tpp) REVERT: E 318 THR cc_start: 0.9372 (m) cc_final: 0.9165 (p) REVERT: E 362 TYR cc_start: 0.8952 (t80) cc_final: 0.8691 (t80) REVERT: F 107 GLU cc_start: 0.7574 (tt0) cc_final: 0.7214 (tt0) REVERT: F 132 MET cc_start: 0.9404 (tmm) cc_final: 0.9159 (tmm) REVERT: F 176 MET cc_start: 0.8925 (tpp) cc_final: 0.8652 (tpp) REVERT: F 283 MET cc_start: 0.9039 (tpp) cc_final: 0.8787 (mmm) REVERT: F 285 CYS cc_start: 0.8958 (m) cc_final: 0.8663 (m) REVERT: A 11 ASP cc_start: 0.9047 (t0) cc_final: 0.6837 (p0) REVERT: A 25 ASP cc_start: 0.9276 (m-30) cc_final: 0.8954 (p0) REVERT: A 59 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8200 (mm-40) REVERT: A 107 GLU cc_start: 0.8977 (tt0) cc_final: 0.8723 (tt0) REVERT: A 176 MET cc_start: 0.9560 (mmm) cc_final: 0.8973 (mpp) REVERT: A 227 MET cc_start: 0.8750 (mmm) cc_final: 0.8472 (mmm) REVERT: A 314 GLN cc_start: 0.9476 (tt0) cc_final: 0.9168 (tm-30) REVERT: A 355 MET cc_start: 0.8704 (mmp) cc_final: 0.8144 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2361 time to fit residues: 75.4502 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 : 1.849 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** 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** F 128 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.043031 restraints weight = 62999.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.044664 restraints weight = 36252.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.045821 restraints weight = 24362.488| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14950 Z= 0.168 Angle : 0.621 6.604 20290 Z= 0.305 Chirality : 0.045 0.164 2255 Planarity : 0.004 0.036 2595 Dihedral : 5.624 49.981 2080 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.64 (0.20), residues: 1845 helix: 0.90 (0.19), residues: 750 sheet: -0.26 (0.30), residues: 310 loop : 0.46 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.016 0.001 PHE F 375 TYR 0.013 0.001 TYR A 143 ARG 0.006 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 698) hydrogen bonds : angle 4.47273 ( 1752) covalent geometry : bond 0.00371 (14950) covalent geometry : angle 0.62112 (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 201 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.8023 (t0) cc_final: 0.7723 (t0) REVERT: C 176 MET cc_start: 0.9154 (tpp) cc_final: 0.8788 (mmm) REVERT: C 205 GLU cc_start: 0.8734 (mp0) cc_final: 0.8364 (mp0) REVERT: D 82 MET cc_start: 0.9201 (tpt) cc_final: 0.8819 (tpp) REVERT: D 107 GLU cc_start: 0.8850 (pt0) cc_final: 0.8538 (pt0) REVERT: D 179 ASP cc_start: 0.8738 (p0) cc_final: 0.8369 (t0) REVERT: D 184 ASP cc_start: 0.9211 (m-30) cc_final: 0.8996 (m-30) REVERT: D 205 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8460 (mt-10) REVERT: D 226 GLU cc_start: 0.9307 (tp30) cc_final: 0.8740 (tp30) REVERT: D 276 GLU cc_start: 0.9156 (tt0) cc_final: 0.8936 (tp30) REVERT: D 313 MET cc_start: 0.9042 (tpp) cc_final: 0.8714 (tpp) REVERT: D 325 MET cc_start: 0.8150 (tpp) cc_final: 0.7561 (tmm) REVERT: D 330 ILE cc_start: 0.9136 (tt) cc_final: 0.8810 (pt) REVERT: D 355 MET cc_start: 0.8759 (mtp) cc_final: 0.8523 (mtp) REVERT: E 12 ASN cc_start: 0.9365 (p0) cc_final: 0.9161 (p0) REVERT: E 81 ASP cc_start: 0.8829 (t70) cc_final: 0.8322 (t70) REVERT: E 128 ASN cc_start: 0.9185 (t0) cc_final: 0.8865 (t0) REVERT: E 154 ASP cc_start: 0.8472 (t0) cc_final: 0.8253 (t0) REVERT: E 176 MET cc_start: 0.9033 (tpp) cc_final: 0.8796 (mmm) REVERT: E 179 ASP cc_start: 0.8307 (p0) cc_final: 0.7697 (t0) REVERT: E 205 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8325 (mt-10) REVERT: E 244 ASP cc_start: 0.7304 (t70) cc_final: 0.7031 (t0) REVERT: E 269 MET cc_start: 0.8813 (tpp) cc_final: 0.8512 (tmm) REVERT: E 313 MET cc_start: 0.9198 (tpp) cc_final: 0.8986 (tpp) REVERT: E 318 THR cc_start: 0.9351 (m) cc_final: 0.9138 (p) REVERT: F 107 GLU cc_start: 0.7634 (tt0) cc_final: 0.7352 (tt0) REVERT: F 132 MET cc_start: 0.9407 (tmm) cc_final: 0.9182 (tmm) REVERT: F 176 MET cc_start: 0.8886 (tpp) cc_final: 0.8645 (tpp) REVERT: F 283 MET cc_start: 0.9059 (tpp) cc_final: 0.8797 (mmm) REVERT: F 285 CYS cc_start: 0.8944 (m) cc_final: 0.8657 (m) REVERT: F 305 MET cc_start: 0.9000 (mmt) cc_final: 0.8358 (mmt) REVERT: A 11 ASP cc_start: 0.9065 (t0) cc_final: 0.8728 (t0) REVERT: A 25 ASP cc_start: 0.9296 (m-30) cc_final: 0.8997 (p0) REVERT: A 59 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 107 GLU cc_start: 0.8988 (tt0) cc_final: 0.8787 (tt0) REVERT: A 176 MET cc_start: 0.9540 (mmm) cc_final: 0.8914 (mpp) REVERT: A 227 MET cc_start: 0.8733 (mmm) cc_final: 0.8445 (mmm) REVERT: A 305 MET cc_start: 0.9123 (mmt) cc_final: 0.8807 (mmm) REVERT: A 314 GLN cc_start: 0.9484 (tt0) cc_final: 0.9161 (tm-30) REVERT: A 355 MET cc_start: 0.8716 (mmp) cc_final: 0.8159 (mmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2172 time to fit residues: 68.9383 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 : 1.667 ------------------------------------------------------------------------------- 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: 1.9990 chunk 159 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.042485 restraints weight = 63371.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.044100 restraints weight = 36560.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.045219 restraints weight = 24700.240| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14950 Z= 0.207 Angle : 0.657 6.660 20290 Z= 0.322 Chirality : 0.046 0.172 2255 Planarity : 0.004 0.035 2595 Dihedral : 5.713 51.406 2080 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.61 (0.20), residues: 1845 helix: 0.83 (0.19), residues: 760 sheet: -0.26 (0.30), residues: 310 loop : 0.48 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.009 0.001 HIS D 73 PHE 0.014 0.001 PHE D 127 TYR 0.013 0.001 TYR A 91 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 698) hydrogen bonds : angle 4.55027 ( 1752) covalent geometry : bond 0.00454 (14950) covalent geometry : angle 0.65665 (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 196 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.8101 (t0) cc_final: 0.7831 (t0) REVERT: C 205 GLU cc_start: 0.8878 (mp0) cc_final: 0.8514 (mp0) REVERT: D 44 MET cc_start: 0.9079 (mmm) cc_final: 0.8873 (mmm) REVERT: D 82 MET cc_start: 0.9263 (tpt) cc_final: 0.8932 (tpt) REVERT: D 107 GLU cc_start: 0.8839 (pt0) cc_final: 0.8538 (pt0) REVERT: D 179 ASP cc_start: 0.8716 (p0) cc_final: 0.8303 (t0) REVERT: D 205 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8462 (mt-10) REVERT: D 226 GLU cc_start: 0.9311 (tp30) cc_final: 0.8714 (tp30) REVERT: D 276 GLU cc_start: 0.9175 (tt0) cc_final: 0.8917 (tp30) REVERT: D 313 MET cc_start: 0.9079 (tpp) cc_final: 0.8768 (tpp) REVERT: D 330 ILE cc_start: 0.9103 (tt) cc_final: 0.8794 (pt) REVERT: E 12 ASN cc_start: 0.9408 (p0) cc_final: 0.9206 (p0) REVERT: E 81 ASP cc_start: 0.8832 (t70) cc_final: 0.8361 (t70) REVERT: E 128 ASN cc_start: 0.9182 (t0) cc_final: 0.8838 (t0) REVERT: E 179 ASP cc_start: 0.8376 (p0) cc_final: 0.7692 (t0) REVERT: E 205 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8301 (mt-10) REVERT: E 244 ASP cc_start: 0.7334 (t70) cc_final: 0.7042 (t0) REVERT: E 269 MET cc_start: 0.8841 (tpp) cc_final: 0.8522 (tmm) REVERT: E 313 MET cc_start: 0.9198 (tpp) cc_final: 0.8977 (tpp) REVERT: E 318 THR cc_start: 0.9361 (m) cc_final: 0.9144 (p) REVERT: F 107 GLU cc_start: 0.7652 (tt0) cc_final: 0.7405 (tt0) REVERT: F 176 MET cc_start: 0.8909 (tpp) cc_final: 0.8650 (tpp) REVERT: F 283 MET cc_start: 0.9079 (tpp) cc_final: 0.8845 (mmm) REVERT: F 285 CYS cc_start: 0.8991 (m) cc_final: 0.8707 (m) REVERT: F 305 MET cc_start: 0.9119 (mmt) cc_final: 0.8575 (mmt) REVERT: F 313 MET cc_start: 0.9138 (tpp) cc_final: 0.8868 (tpp) REVERT: F 355 MET cc_start: 0.8532 (mtm) cc_final: 0.8330 (ttm) REVERT: F 375 PHE cc_start: 0.7638 (t80) cc_final: 0.7331 (m-10) REVERT: A 25 ASP cc_start: 0.9317 (m-30) cc_final: 0.9043 (p0) REVERT: A 59 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8307 (mm-40) REVERT: A 176 MET cc_start: 0.9530 (mmm) cc_final: 0.8866 (mpp) REVERT: A 227 MET cc_start: 0.8738 (mmm) cc_final: 0.8462 (mmm) REVERT: A 314 GLN cc_start: 0.9501 (tt0) cc_final: 0.9177 (tm-30) REVERT: A 355 MET cc_start: 0.8720 (mmp) cc_final: 0.8125 (mmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2259 time to fit residues: 69.7535 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 : 1.802 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 173 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- 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** F 128 ASN ** 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 = 0.2904 r_free = 0.2904 target = 0.056207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.042900 restraints weight = 63001.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.044500 restraints weight = 36840.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.045576 restraints weight = 24692.833| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14950 Z= 0.198 Angle : 0.654 9.069 20290 Z= 0.318 Chirality : 0.046 0.195 2255 Planarity : 0.004 0.036 2595 Dihedral : 5.707 49.046 2080 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.69 (0.20), residues: 1845 helix: 0.89 (0.19), residues: 760 sheet: -0.11 (0.30), residues: 320 loop : 0.49 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.013 0.001 PHE D 223 TYR 0.013 0.001 TYR A 91 ARG 0.004 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 698) hydrogen bonds : angle 4.53797 ( 1752) covalent geometry : bond 0.00436 (14950) covalent geometry : angle 0.65379 (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 191 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7169 (ptm) cc_final: 0.6754 (ptm) REVERT: C 154 ASP cc_start: 0.8008 (t0) cc_final: 0.7739 (t0) REVERT: C 205 GLU cc_start: 0.8955 (mp0) cc_final: 0.8597 (mp0) REVERT: C 227 MET cc_start: 0.9222 (mmm) cc_final: 0.8911 (mmm) REVERT: D 82 MET cc_start: 0.9226 (tpt) cc_final: 0.8922 (tpt) REVERT: D 107 GLU cc_start: 0.8771 (pt0) cc_final: 0.8508 (pt0) REVERT: D 179 ASP cc_start: 0.8740 (p0) cc_final: 0.8257 (t0) REVERT: D 276 GLU cc_start: 0.9106 (tt0) cc_final: 0.8896 (tp30) REVERT: D 313 MET cc_start: 0.9082 (tpp) cc_final: 0.8788 (tpp) REVERT: D 330 ILE cc_start: 0.9141 (tt) cc_final: 0.8817 (pt) REVERT: E 12 ASN cc_start: 0.9365 (p0) cc_final: 0.9129 (p0) REVERT: E 128 ASN cc_start: 0.9122 (t0) cc_final: 0.8791 (t0) REVERT: E 176 MET cc_start: 0.8989 (tpp) cc_final: 0.8721 (mmm) REVERT: E 179 ASP cc_start: 0.8353 (p0) cc_final: 0.7699 (t0) REVERT: E 205 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8335 (mt-10) REVERT: E 244 ASP cc_start: 0.7327 (t0) cc_final: 0.7036 (t0) REVERT: E 313 MET cc_start: 0.9137 (tpp) cc_final: 0.8937 (tpp) REVERT: F 107 GLU cc_start: 0.7523 (tt0) cc_final: 0.7294 (tt0) REVERT: F 205 GLU cc_start: 0.8996 (pm20) cc_final: 0.8753 (pm20) REVERT: F 283 MET cc_start: 0.9073 (tpp) cc_final: 0.8873 (mmm) REVERT: F 285 CYS cc_start: 0.8945 (m) cc_final: 0.8696 (m) REVERT: F 305 MET cc_start: 0.9054 (mmt) cc_final: 0.8532 (mmt) REVERT: F 355 MET cc_start: 0.8492 (mtm) cc_final: 0.8209 (ttm) REVERT: A 59 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8327 (mm-40) REVERT: A 176 MET cc_start: 0.9516 (mmm) cc_final: 0.8837 (mpp) REVERT: A 227 MET cc_start: 0.8727 (mmm) cc_final: 0.8453 (mmm) REVERT: A 314 GLN cc_start: 0.9496 (tt0) cc_final: 0.9172 (tm-30) REVERT: A 353 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8726 (mm-40) REVERT: A 355 MET cc_start: 0.8722 (mmp) cc_final: 0.8164 (mmm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2195 time to fit residues: 65.3321 Evaluate side-chains 148 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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: 6.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 128 ASN 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 = 0.2915 r_free = 0.2915 target = 0.056620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.043039 restraints weight = 62484.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.044685 restraints weight = 36086.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.045829 restraints weight = 24285.163| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.6364 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= 0.162 Angle : 0.643 8.360 20290 Z= 0.313 Chirality : 0.046 0.175 2255 Planarity : 0.004 0.035 2595 Dihedral : 5.628 53.492 2080 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.76 (0.20), residues: 1845 helix: 0.94 (0.19), residues: 760 sheet: -0.02 (0.31), residues: 310 loop : 0.50 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.010 0.001 PHE D 266 TYR 0.024 0.001 TYR C 143 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 698) hydrogen bonds : angle 4.52185 ( 1752) covalent geometry : bond 0.00363 (14950) covalent geometry : angle 0.64311 (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 188 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: C 47 MET cc_start: 0.7184 (ptm) cc_final: 0.6403 (ptm) REVERT: C 154 ASP cc_start: 0.8023 (t0) cc_final: 0.7693 (t0) REVERT: C 205 GLU cc_start: 0.8905 (mp0) cc_final: 0.8550 (mp0) REVERT: C 227 MET cc_start: 0.9192 (mmm) cc_final: 0.8866 (mmm) REVERT: C 305 MET cc_start: 0.9441 (mtp) cc_final: 0.8885 (mtt) REVERT: D 82 MET cc_start: 0.9181 (tpt) cc_final: 0.8833 (tpp) REVERT: D 107 GLU cc_start: 0.8795 (pt0) cc_final: 0.8485 (pt0) REVERT: D 179 ASP cc_start: 0.8684 (p0) cc_final: 0.8240 (t0) REVERT: D 184 ASP cc_start: 0.9157 (m-30) cc_final: 0.8935 (m-30) REVERT: D 257 CYS cc_start: 0.9214 (t) cc_final: 0.9006 (t) REVERT: D 313 MET cc_start: 0.9068 (tpp) cc_final: 0.8783 (tpp) REVERT: D 330 ILE cc_start: 0.9115 (tt) cc_final: 0.8816 (pt) REVERT: E 12 ASN cc_start: 0.9388 (p0) cc_final: 0.9176 (p0) REVERT: E 128 ASN cc_start: 0.9139 (t0) cc_final: 0.8811 (t0) REVERT: E 176 MET cc_start: 0.9057 (tpp) cc_final: 0.8800 (mmm) REVERT: E 179 ASP cc_start: 0.8310 (p0) cc_final: 0.7658 (t0) REVERT: E 205 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8431 (mt-10) REVERT: E 227 MET cc_start: 0.9277 (mmp) cc_final: 0.9076 (mmm) REVERT: E 244 ASP cc_start: 0.7357 (t0) cc_final: 0.6937 (t0) REVERT: E 313 MET cc_start: 0.9197 (tpp) cc_final: 0.8985 (tpp) REVERT: F 205 GLU cc_start: 0.8979 (pm20) cc_final: 0.8712 (pm20) REVERT: F 283 MET cc_start: 0.9055 (tpp) cc_final: 0.8768 (mmm) REVERT: F 285 CYS cc_start: 0.8960 (m) cc_final: 0.8692 (m) REVERT: F 305 MET cc_start: 0.9123 (mmt) cc_final: 0.8547 (mmt) REVERT: F 355 MET cc_start: 0.8568 (mtm) cc_final: 0.8350 (ttm) REVERT: F 375 PHE cc_start: 0.7614 (t80) cc_final: 0.7409 (m-10) REVERT: A 59 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8295 (mm-40) REVERT: A 95 ARG cc_start: 0.9215 (pmt170) cc_final: 0.9011 (mpp80) REVERT: A 176 MET cc_start: 0.9478 (mmm) cc_final: 0.8776 (mpp) REVERT: A 227 MET cc_start: 0.8659 (mmm) cc_final: 0.8393 (mmm) REVERT: A 287 ILE cc_start: 0.9216 (tt) cc_final: 0.8971 (mt) REVERT: A 314 GLN cc_start: 0.9475 (tt0) cc_final: 0.9161 (tm-30) REVERT: A 353 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8731 (mm-40) REVERT: A 355 MET cc_start: 0.8704 (mmp) cc_final: 0.8118 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2164 time to fit residues: 64.1187 Evaluate side-chains 146 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 46 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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** E 225 ASN ** 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 = 0.2919 r_free = 0.2919 target = 0.056838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.043262 restraints weight = 62527.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.044897 restraints weight = 36102.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.046047 restraints weight = 24325.243| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14950 Z= 0.157 Angle : 0.641 8.589 20290 Z= 0.311 Chirality : 0.046 0.180 2255 Planarity : 0.004 0.033 2595 Dihedral : 5.592 57.237 2080 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.76 (0.20), residues: 1845 helix: 0.94 (0.19), residues: 760 sheet: -0.01 (0.31), residues: 310 loop : 0.50 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 86 HIS 0.008 0.001 HIS D 73 PHE 0.012 0.001 PHE D 266 TYR 0.022 0.001 TYR C 143 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 698) hydrogen bonds : angle 4.48195 ( 1752) covalent geometry : bond 0.00351 (14950) covalent geometry : angle 0.64144 (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 191 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7183 (ptm) cc_final: 0.6780 (ptp) REVERT: C 78 ASN cc_start: 0.8954 (t0) cc_final: 0.8498 (t0) REVERT: C 154 ASP cc_start: 0.8072 (t0) cc_final: 0.7775 (t0) REVERT: C 176 MET cc_start: 0.9133 (tpp) cc_final: 0.8727 (mmm) REVERT: C 205 GLU cc_start: 0.8898 (mp0) cc_final: 0.8560 (mp0) REVERT: C 225 ASN cc_start: 0.8954 (m110) cc_final: 0.8751 (t0) REVERT: C 227 MET cc_start: 0.9201 (mmm) cc_final: 0.8786 (mmm) REVERT: C 252 ASN cc_start: 0.9418 (m-40) cc_final: 0.9128 (p0) REVERT: C 305 MET cc_start: 0.9428 (mtp) cc_final: 0.8875 (mtt) REVERT: D 82 MET cc_start: 0.9252 (tpt) cc_final: 0.8649 (tpp) REVERT: D 107 GLU cc_start: 0.8764 (pt0) cc_final: 0.8487 (pt0) REVERT: D 179 ASP cc_start: 0.8764 (p0) cc_final: 0.8243 (t0) REVERT: D 184 ASP cc_start: 0.9148 (m-30) cc_final: 0.8919 (m-30) REVERT: D 257 CYS cc_start: 0.9247 (t) cc_final: 0.9044 (t) REVERT: D 313 MET cc_start: 0.9054 (tpp) cc_final: 0.8786 (tpp) REVERT: D 325 MET cc_start: 0.8285 (mmm) cc_final: 0.7865 (mmm) REVERT: D 330 ILE cc_start: 0.9106 (tt) cc_final: 0.8825 (pt) REVERT: E 12 ASN cc_start: 0.9394 (p0) cc_final: 0.9159 (p0) REVERT: E 128 ASN cc_start: 0.9099 (t0) cc_final: 0.8777 (t0) REVERT: E 176 MET cc_start: 0.9024 (tpp) cc_final: 0.8720 (mmm) REVERT: E 179 ASP cc_start: 0.8272 (p0) cc_final: 0.7641 (t0) REVERT: E 205 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8452 (mt-10) REVERT: F 82 MET cc_start: 0.9083 (tpt) cc_final: 0.8851 (tpt) REVERT: F 205 GLU cc_start: 0.8982 (pm20) cc_final: 0.8709 (pm20) REVERT: F 285 CYS cc_start: 0.8961 (m) cc_final: 0.8678 (m) REVERT: F 305 MET cc_start: 0.9135 (mmt) cc_final: 0.8558 (mmt) REVERT: F 313 MET cc_start: 0.9125 (tpp) cc_final: 0.8854 (tpp) REVERT: F 355 MET cc_start: 0.8574 (mtm) cc_final: 0.8361 (ttm) REVERT: A 59 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 95 ARG cc_start: 0.9242 (pmt170) cc_final: 0.9036 (mpp80) REVERT: A 176 MET cc_start: 0.9459 (mmm) cc_final: 0.8762 (mpp) REVERT: A 227 MET cc_start: 0.8671 (mmm) cc_final: 0.8365 (mmm) REVERT: A 287 ILE cc_start: 0.9217 (tt) cc_final: 0.8993 (mt) REVERT: A 305 MET cc_start: 0.9143 (mmt) cc_final: 0.8924 (mmt) REVERT: A 314 GLN cc_start: 0.9480 (tt0) cc_final: 0.9152 (tm-30) REVERT: A 355 MET cc_start: 0.8715 (mmp) cc_final: 0.8149 (mmm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2289 time to fit residues: 69.1465 Evaluate side-chains 151 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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: 0.0970 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.0780 ------------------------------------------------------------------------------- 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** F 128 ASN ** A 59 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.044619 restraints weight = 61458.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.046324 restraints weight = 34808.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.047502 restraints weight = 23145.630| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14950 Z= 0.103 Angle : 0.617 8.574 20290 Z= 0.295 Chirality : 0.045 0.170 2255 Planarity : 0.004 0.050 2595 Dihedral : 5.342 56.356 2080 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1845 helix: 1.35 (0.20), residues: 720 sheet: -0.02 (0.30), residues: 325 loop : 0.59 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 86 HIS 0.006 0.001 HIS D 73 PHE 0.009 0.001 PHE D 266 TYR 0.018 0.001 TYR C 143 ARG 0.005 0.000 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 698) hydrogen bonds : angle 4.36942 ( 1752) covalent geometry : bond 0.00232 (14950) covalent geometry : angle 0.61740 (20290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.91 seconds wall clock time: 70 minutes 59.81 seconds (4259.81 seconds total)