Starting phenix.real_space_refine on Thu Aug 6 06:42:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.map" model { file = "/net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ves_43173/08_2026/8ves_43173.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 18 5.49 5 S 60 5.16 5 C 8850 2.51 5 N 2579 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14303 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2327 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2327 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "B" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2327 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "E" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2327 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "D" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2327 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "F" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2258 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 1 Chain: "H" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 408 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.23 Number of scatterers: 14303 At special positions: 0 Unit cell: (85.6, 85.6, 156.22, 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 60 16.00 P 18 15.00 O 2796 8.00 N 2579 7.00 C 8850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 608.5 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 67.9% alpha, 10.5% beta 5 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.559A pdb=" N ARG A 43 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 124 through 190 removed outlier: 3.877A pdb=" N ALA A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.626A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 Processing helix chain 'A' and resid 262 through 284 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.793A pdb=" N ARG C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 100 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 122 through 172 removed outlier: 3.699A pdb=" N ILE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 195 removed outlier: 3.514A pdb=" N LYS C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 213 through 232 Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.599A pdb=" N GLN C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.646A pdb=" N GLN C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 81 through 100 removed outlier: 3.518A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 123 through 192 removed outlier: 3.979A pdb=" N ALA B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 197 through 213 Processing helix chain 'B' and resid 214 through 234 Processing helix chain 'B' and resid 239 through 260 Processing helix chain 'B' and resid 262 through 284 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.639A pdb=" N ARG E 43 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER E 44 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 81 through 100 removed outlier: 3.614A pdb=" N GLN E 98 " --> pdb=" O TRP E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'E' and resid 124 through 174 removed outlier: 3.559A pdb=" N ALA E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.668A pdb=" N ASP E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 208 removed outlier: 3.655A pdb=" N GLN E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 removed outlier: 4.159A pdb=" N ILE E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 232 removed outlier: 3.505A pdb=" N LYS E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 260 removed outlier: 3.868A pdb=" N GLN E 247 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU E 248 " --> pdb=" O PHE E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 284 removed outlier: 3.621A pdb=" N GLN E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.630A pdb=" N GLN D 98 " --> pdb=" O TRP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 122 through 192 removed outlier: 4.509A pdb=" N ILE D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.943A pdb=" N ARG D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 212 removed outlier: 3.761A pdb=" N LEU D 207 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 232 Processing helix chain 'D' and resid 238 through 260 removed outlier: 3.735A pdb=" N GLN D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 284 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.760A pdb=" N ARG F 43 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER F 44 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 81 through 100 removed outlier: 3.531A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN F 98 " --> pdb=" O TRP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'F' and resid 124 through 172 removed outlier: 3.547A pdb=" N GLU F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 192 removed outlier: 4.288A pdb=" N ALA F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 211 removed outlier: 4.005A pdb=" N LEU F 207 " --> pdb=" O GLN F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.574A pdb=" N LYS F 233 " --> pdb=" O TYR F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 259 removed outlier: 4.118A pdb=" N THR F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 284 removed outlier: 3.534A pdb=" N GLN F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 15 removed outlier: 3.729A pdb=" N ALA A 7 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 19 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 8 through 15 removed outlier: 6.274A pdb=" N GLU C 33 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS C 64 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 35 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU C 66 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG C 37 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TYR C 68 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 14 removed outlier: 6.275A pdb=" N GLU B 33 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS B 64 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 35 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 66 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG B 37 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TYR B 68 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 15 removed outlier: 3.511A pdb=" N ALA E 7 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 8 through 14 Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.538A pdb=" N ALA D 117 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 7 through 14 990 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.61 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: 4034 1.33 - 1.45: 2039 1.45 - 1.57: 8289 1.57 - 1.69: 35 1.69 - 1.81: 114 Bond restraints: 14511 Sorted by residual: bond pdb=" C4 C H 3 " pdb=" C5 C H 3 " ideal model delta sigma weight residual 1.425 1.417 0.008 8.00e-03 1.56e+04 1.08e+00 bond pdb=" N9 G H 1 " pdb=" C4 G H 1 " ideal model delta sigma weight residual 1.375 1.367 0.008 8.00e-03 1.56e+04 9.28e-01 bond pdb=" C4 U H 14 " pdb=" C5 U H 14 " ideal model delta sigma weight residual 1.431 1.422 0.009 9.00e-03 1.23e+04 9.05e-01 bond pdb=" CG1 ILE F 156 " pdb=" CD1 ILE F 156 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.57e-01 bond pdb=" C5 G H 15 " pdb=" C4 G H 15 " ideal model delta sigma weight residual 1.379 1.373 0.006 7.00e-03 2.04e+04 8.48e-01 ... (remaining 14506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 19218 1.05 - 2.11: 326 2.11 - 3.16: 86 3.16 - 4.21: 7 4.21 - 5.26: 14 Bond angle restraints: 19651 Sorted by residual: angle pdb=" O5' A H 4 " pdb=" C5' A H 4 " pdb=" C4' A H 4 " ideal model delta sigma weight residual 109.40 112.50 -3.10 8.00e-01 1.56e+00 1.50e+01 angle pdb=" C1' U H 14 " pdb=" N1 U H 14 " pdb=" C2 U H 14 " ideal model delta sigma weight residual 117.70 122.26 -4.56 1.20e+00 6.94e-01 1.44e+01 angle pdb=" O5' A H 7 " pdb=" C5' A H 7 " pdb=" C4' A H 7 " ideal model delta sigma weight residual 109.40 112.29 -2.89 8.00e-01 1.56e+00 1.30e+01 angle pdb=" O5' U H 14 " pdb=" C5' U H 14 " pdb=" C4' U H 14 " ideal model delta sigma weight residual 109.40 111.90 -2.50 8.00e-01 1.56e+00 9.73e+00 angle pdb=" O5' G H 5 " pdb=" C5' G H 5 " pdb=" C4' G H 5 " ideal model delta sigma weight residual 109.40 111.86 -2.46 8.00e-01 1.56e+00 9.45e+00 ... (remaining 19646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.81: 8410 18.81 - 37.63: 540 37.63 - 56.44: 98 56.44 - 75.25: 32 75.25 - 94.07: 3 Dihedral angle restraints: 9083 sinusoidal: 4038 harmonic: 5045 Sorted by residual: dihedral pdb=" O4' A H 18 " pdb=" C1' A H 18 " pdb=" N9 A H 18 " pdb=" C4 A H 18 " ideal model delta sinusoidal sigma weight residual -78.00 -6.71 -71.29 1 1.70e+01 3.46e-03 2.26e+01 dihedral pdb=" CB MET D 245 " pdb=" CG MET D 245 " pdb=" SD MET D 245 " pdb=" CE MET D 245 " ideal model delta sinusoidal sigma weight residual -180.00 -121.44 -58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET C 246 " pdb=" CG MET C 246 " pdb=" SD MET C 246 " pdb=" CE MET C 246 " ideal model delta sinusoidal sigma weight residual 60.00 114.73 -54.73 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 9080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1616 0.033 - 0.066: 496 0.066 - 0.099: 81 0.099 - 0.131: 48 0.131 - 0.164: 9 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE F 13 " pdb=" CA ILE F 13 " pdb=" CG1 ILE F 13 " pdb=" CG2 ILE F 13 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C2' G H 12 " pdb=" C3' G H 12 " pdb=" O2' G H 12 " pdb=" C1' G H 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" C2' A H 4 " pdb=" C3' A H 4 " pdb=" O2' A H 4 " pdb=" C1' A H 4 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2247 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 11 " 0.145 9.50e-02 1.11e+02 6.53e-02 2.78e+00 pdb=" NE ARG F 11 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 11 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 11 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 11 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 13 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ILE F 13 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE F 13 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS F 14 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP F 112 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO F 113 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 113 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 113 " -0.015 5.00e-02 4.00e+02 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 259 2.71 - 3.25: 14148 3.25 - 3.80: 22280 3.80 - 4.35: 28891 4.35 - 4.90: 48238 Nonbonded interactions: 113816 Sorted by model distance: nonbonded pdb=" NH1 ARG F 145 " pdb=" OE1 GLU F 287 " model vdw 2.158 3.120 nonbonded pdb=" O MET F 5 " pdb=" OG SER F 26 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR C 8 " pdb=" OE2 GLU C 23 " model vdw 2.262 3.040 nonbonded pdb=" O MET D 5 " pdb=" OG SER D 26 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG E 145 " pdb=" OE1 GLU E 287 " model vdw 2.281 3.120 ... (remaining 113811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 192 or resid 201 through 287)) selection = (chain 'B' and (resid 1 through 192 or resid 201 through 287)) selection = (chain 'C' and (resid 1 through 192 or resid 201 through 287)) selection = (chain 'D' and (resid 1 through 192 or resid 201 through 287)) selection = (chain 'E' and (resid 1 through 192 or resid 201 through 287)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14511 Z= 0.143 Angle : 0.397 5.263 19651 Z= 0.234 Chirality : 0.036 0.164 2250 Planarity : 0.003 0.065 2500 Dihedral : 13.073 94.065 5775 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.20), residues: 1700 helix: 2.12 (0.15), residues: 1110 sheet: 1.92 (0.36), residues: 201 loop : -0.34 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 11 TYR 0.006 0.001 TYR A 68 PHE 0.014 0.002 PHE F 249 TRP 0.007 0.001 TRP F 22 HIS 0.002 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14511) covalent geometry : angle 0.39656 / 0.23 (19651) hydrogen bonds : bond 0.20425 / 13.48 ( 1002) hydrogen bonds : angle 5.52968 / 3.96 ( 2956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8168 (mmm160) REVERT: A 77 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7186 (tp30) REVERT: A 158 GLN cc_start: 0.8703 (tt0) cc_final: 0.8455 (tt0) REVERT: A 193 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7517 (mp10) REVERT: A 202 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7474 (mp0) REVERT: C 40 GLU cc_start: 0.7924 (tp30) cc_final: 0.7722 (tp30) REVERT: C 81 ASN cc_start: 0.8272 (t0) cc_final: 0.7639 (t0) REVERT: C 184 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7868 (tpt-90) REVERT: C 281 GLU cc_start: 0.8588 (tt0) cc_final: 0.8318 (tt0) REVERT: B 108 ASP cc_start: 0.8914 (m-30) cc_final: 0.8683 (m-30) REVERT: B 219 ASP cc_start: 0.8361 (t0) cc_final: 0.8110 (t0) REVERT: B 246 MET cc_start: 0.8641 (mmm) cc_final: 0.8021 (mmp) REVERT: E 178 LEU cc_start: 0.7810 (mt) cc_final: 0.7493 (mt) REVERT: E 179 GLN cc_start: 0.7242 (mm110) cc_final: 0.6735 (tt0) REVERT: E 202 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7313 (mm-30) REVERT: E 203 GLN cc_start: 0.7950 (mt0) cc_final: 0.7682 (mp10) REVERT: E 243 ASP cc_start: 0.9168 (t0) cc_final: 0.8822 (t0) REVERT: D 50 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7694 (ttt90) REVERT: D 122 ASP cc_start: 0.8061 (t0) cc_final: 0.7852 (t70) REVERT: F 1 MET cc_start: 0.7671 (ptp) cc_final: 0.7358 (ptt) REVERT: F 40 GLU cc_start: 0.8746 (tp30) cc_final: 0.8328 (tp30) REVERT: F 178 LEU cc_start: 0.8466 (mt) cc_final: 0.8248 (mt) REVERT: F 207 LEU cc_start: 0.7226 (pp) cc_final: 0.7025 (pp) REVERT: F 216 GLU cc_start: 0.8136 (tt0) cc_final: 0.7857 (mt-10) REVERT: F 247 GLN cc_start: 0.8098 (tp40) cc_final: 0.7877 (mt0) REVERT: F 271 GLU cc_start: 0.8556 (tp30) cc_final: 0.8282 (tp30) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1440 time to fit residues: 64.8687 Evaluate side-chains 206 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 224 HIS B 173 HIS E 179 GLN E 285 ASN D 247 GLN F 173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108015 restraints weight = 17700.500| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.30 r_work: 0.3132 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14511 Z= 0.161 Angle : 0.505 6.008 19651 Z= 0.274 Chirality : 0.036 0.141 2250 Planarity : 0.004 0.057 2500 Dihedral : 8.802 93.674 2165 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.94 % Allowed : 5.43 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.20), residues: 1700 helix: 2.63 (0.14), residues: 1119 sheet: 2.43 (0.37), residues: 199 loop : -0.40 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 11 TYR 0.007 0.001 TYR A 68 PHE 0.015 0.002 PHE E 141 TRP 0.011 0.001 TRP F 94 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14511) covalent geometry : angle 0.50457 / 0.27 (19651) hydrogen bonds : bond 0.06238 / 4.15 ( 1002) hydrogen bonds : angle 4.11080 / 2.93 ( 2956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: A 67 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8031 (mmm160) REVERT: A 77 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7140 (tp30) REVERT: A 202 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7403 (mp0) REVERT: C 40 GLU cc_start: 0.7982 (tp30) cc_final: 0.7739 (tp30) REVERT: C 174 MET cc_start: 0.8367 (tpp) cc_final: 0.7926 (mmm) REVERT: C 184 ARG cc_start: 0.8338 (tpp-160) cc_final: 0.7930 (tpt-90) REVERT: C 246 MET cc_start: 0.8824 (mmp) cc_final: 0.8131 (mmp) REVERT: C 279 MET cc_start: 0.8839 (ttm) cc_final: 0.8582 (mtm) REVERT: C 281 GLU cc_start: 0.8659 (tt0) cc_final: 0.8279 (tt0) REVERT: B 69 GLU cc_start: 0.8143 (tt0) cc_final: 0.7919 (tt0) REVERT: B 219 ASP cc_start: 0.8406 (t0) cc_final: 0.8177 (t0) REVERT: B 246 MET cc_start: 0.8571 (mmm) cc_final: 0.7754 (mmp) REVERT: E 202 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 243 ASP cc_start: 0.9051 (t0) cc_final: 0.8708 (t0) REVERT: D 122 ASP cc_start: 0.8075 (t0) cc_final: 0.7811 (t70) REVERT: F 21 THR cc_start: 0.9112 (m) cc_final: 0.8884 (p) REVERT: F 40 GLU cc_start: 0.8661 (tp30) cc_final: 0.8244 (tp30) REVERT: F 174 MET cc_start: 0.7850 (tpt) cc_final: 0.7315 (tpt) REVERT: F 179 GLN cc_start: 0.7690 (mt0) cc_final: 0.7189 (tp-100) REVERT: F 271 GLU cc_start: 0.8528 (tp30) cc_final: 0.8053 (tp30) outliers start: 14 outliers final: 7 residues processed: 217 average time/residue: 0.1383 time to fit residues: 42.0733 Evaluate side-chains 183 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108790 restraints weight = 17798.518| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.31 r_work: 0.3136 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14511 Z= 0.134 Angle : 0.468 8.969 19651 Z= 0.247 Chirality : 0.035 0.211 2250 Planarity : 0.003 0.029 2500 Dihedral : 8.676 92.615 2165 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.07 % Allowed : 7.04 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.20), residues: 1700 helix: 2.76 (0.14), residues: 1121 sheet: 2.33 (0.36), residues: 202 loop : -0.44 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 43 TYR 0.006 0.001 TYR A 68 PHE 0.014 0.001 PHE E 141 TRP 0.012 0.001 TRP E 180 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14511) covalent geometry : angle 0.46788 / 0.25 (19651) hydrogen bonds : bond 0.05252 / 3.49 ( 1002) hydrogen bonds : angle 3.84107 / 2.73 ( 2956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: A 67 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7958 (mmm160) REVERT: A 77 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7112 (tp30) REVERT: A 202 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7324 (mp0) REVERT: A 227 GLU cc_start: 0.8192 (tp30) cc_final: 0.7643 (tt0) REVERT: A 246 MET cc_start: 0.8851 (mmt) cc_final: 0.8523 (mmt) REVERT: C 40 GLU cc_start: 0.7974 (tp30) cc_final: 0.7727 (tp30) REVERT: C 174 MET cc_start: 0.8221 (tpp) cc_final: 0.7851 (mmm) REVERT: C 184 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7858 (tpt-90) REVERT: C 246 MET cc_start: 0.8858 (mmp) cc_final: 0.8148 (mmp) REVERT: C 281 GLU cc_start: 0.8666 (tt0) cc_final: 0.8405 (tt0) REVERT: B 69 GLU cc_start: 0.8209 (tt0) cc_final: 0.8006 (tt0) REVERT: B 219 ASP cc_start: 0.8377 (t0) cc_final: 0.8169 (t0) REVERT: B 246 MET cc_start: 0.8749 (mmm) cc_final: 0.7957 (mmp) REVERT: E 201 LEU cc_start: 0.7559 (tp) cc_final: 0.7279 (tp) REVERT: E 203 GLN cc_start: 0.8219 (tt0) cc_final: 0.7650 (tm-30) REVERT: E 205 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7628 (mp) REVERT: D 122 ASP cc_start: 0.8001 (t0) cc_final: 0.7687 (t70) REVERT: F 21 THR cc_start: 0.9093 (m) cc_final: 0.8797 (p) REVERT: F 40 GLU cc_start: 0.8682 (tp30) cc_final: 0.8254 (tp30) REVERT: F 174 MET cc_start: 0.7662 (tpt) cc_final: 0.7318 (tpt) REVERT: F 176 GLU cc_start: 0.7927 (tp30) cc_final: 0.7716 (tp30) REVERT: F 179 GLN cc_start: 0.7636 (mt0) cc_final: 0.7121 (tp-100) REVERT: F 271 GLU cc_start: 0.8488 (tp30) cc_final: 0.7995 (tp30) outliers start: 16 outliers final: 9 residues processed: 196 average time/residue: 0.1376 time to fit residues: 37.7460 Evaluate side-chains 190 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 145 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110736 restraints weight = 17734.929| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.29 r_work: 0.3175 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14511 Z= 0.113 Angle : 0.440 7.094 19651 Z= 0.233 Chirality : 0.034 0.142 2250 Planarity : 0.003 0.037 2500 Dihedral : 8.602 91.821 2165 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.27 % Allowed : 8.24 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.20), residues: 1700 helix: 2.95 (0.14), residues: 1120 sheet: 2.21 (0.35), residues: 209 loop : -0.44 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.006 0.001 TYR C 68 PHE 0.013 0.001 PHE E 141 TRP 0.017 0.001 TRP E 180 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14511) covalent geometry : angle 0.44035 / 0.23 (19651) hydrogen bonds : bond 0.04452 / 2.96 ( 1002) hydrogen bonds : angle 3.62480 / 2.58 ( 2956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7930 (mmm160) REVERT: A 77 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7211 (tp30) REVERT: A 202 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7283 (mp0) REVERT: C 40 GLU cc_start: 0.7973 (tp30) cc_final: 0.7711 (tp30) REVERT: C 174 MET cc_start: 0.8272 (tpp) cc_final: 0.7958 (mmm) REVERT: C 184 ARG cc_start: 0.8279 (tpp-160) cc_final: 0.7960 (tpt-90) REVERT: C 246 MET cc_start: 0.8931 (mmp) cc_final: 0.8455 (mmp) REVERT: C 281 GLU cc_start: 0.8699 (tt0) cc_final: 0.8354 (tt0) REVERT: B 69 GLU cc_start: 0.8176 (tt0) cc_final: 0.7949 (tt0) REVERT: B 219 ASP cc_start: 0.8282 (t0) cc_final: 0.8075 (t0) REVERT: B 246 MET cc_start: 0.8808 (mmm) cc_final: 0.8125 (mmp) REVERT: E 184 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6919 (ttt-90) REVERT: E 201 LEU cc_start: 0.7627 (tp) cc_final: 0.7245 (tp) REVERT: E 203 GLN cc_start: 0.8244 (tt0) cc_final: 0.7663 (tm-30) REVERT: E 205 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7587 (mp) REVERT: E 243 ASP cc_start: 0.8915 (t0) cc_final: 0.8553 (t0) REVERT: D 103 GLU cc_start: 0.8019 (pt0) cc_final: 0.7688 (mt-10) REVERT: D 122 ASP cc_start: 0.7930 (t0) cc_final: 0.7534 (t70) REVERT: D 126 ILE cc_start: 0.5925 (tp) cc_final: 0.5575 (pt) REVERT: F 40 GLU cc_start: 0.8661 (tp30) cc_final: 0.8224 (tp30) REVERT: F 174 MET cc_start: 0.7725 (tpt) cc_final: 0.7481 (tpt) REVERT: F 176 GLU cc_start: 0.7861 (tp30) cc_final: 0.7602 (tp30) REVERT: F 179 GLN cc_start: 0.7729 (mt0) cc_final: 0.7256 (tp-100) REVERT: F 271 GLU cc_start: 0.8535 (tp30) cc_final: 0.8075 (tp30) outliers start: 19 outliers final: 8 residues processed: 209 average time/residue: 0.1323 time to fit residues: 38.5522 Evaluate side-chains 184 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS F 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107032 restraints weight = 17909.209| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.31 r_work: 0.3112 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14511 Z= 0.186 Angle : 0.489 7.774 19651 Z= 0.255 Chirality : 0.036 0.155 2250 Planarity : 0.003 0.045 2500 Dihedral : 8.654 89.309 2165 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.07 % Allowed : 9.72 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.20), residues: 1700 helix: 2.82 (0.14), residues: 1126 sheet: 2.21 (0.35), residues: 202 loop : -0.49 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 59 TYR 0.007 0.001 TYR A 68 PHE 0.017 0.002 PHE E 141 TRP 0.018 0.001 TRP D 180 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (14511) covalent geometry : angle 0.48908 / 0.25 (19651) hydrogen bonds : bond 0.04791 / 3.18 ( 1002) hydrogen bonds : angle 3.68007 / 2.62 ( 2956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7976 (mmm160) REVERT: A 77 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7104 (tp30) REVERT: A 202 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7265 (mp0) REVERT: A 261 ILE cc_start: 0.9467 (tp) cc_final: 0.9247 (tp) REVERT: C 40 GLU cc_start: 0.7999 (tp30) cc_final: 0.7755 (tp30) REVERT: C 174 MET cc_start: 0.8206 (tpp) cc_final: 0.7858 (mmm) REVERT: C 184 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7920 (tpt-90) REVERT: C 246 MET cc_start: 0.9009 (mmp) cc_final: 0.8698 (mmp) REVERT: C 281 GLU cc_start: 0.8710 (tt0) cc_final: 0.8487 (tt0) REVERT: B 63 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 69 GLU cc_start: 0.8185 (tt0) cc_final: 0.7982 (tt0) REVERT: E 203 GLN cc_start: 0.8238 (tt0) cc_final: 0.7733 (tm-30) REVERT: D 103 GLU cc_start: 0.8100 (pt0) cc_final: 0.7764 (mt-10) REVERT: D 122 ASP cc_start: 0.7953 (t0) cc_final: 0.7597 (t70) REVERT: D 126 ILE cc_start: 0.5808 (tp) cc_final: 0.5466 (pt) REVERT: F 40 GLU cc_start: 0.8716 (tp30) cc_final: 0.8274 (tp30) REVERT: F 179 GLN cc_start: 0.7750 (mt0) cc_final: 0.7174 (tp-100) REVERT: F 271 GLU cc_start: 0.8507 (tp30) cc_final: 0.8018 (tp30) outliers start: 16 outliers final: 9 residues processed: 185 average time/residue: 0.1246 time to fit residues: 32.3294 Evaluate side-chains 178 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108271 restraints weight = 17756.625| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.29 r_work: 0.3139 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14511 Z= 0.143 Angle : 0.460 7.340 19651 Z= 0.241 Chirality : 0.035 0.165 2250 Planarity : 0.003 0.047 2500 Dihedral : 8.649 89.691 2165 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.34 % Allowed : 9.72 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.20), residues: 1700 helix: 2.89 (0.14), residues: 1124 sheet: 2.22 (0.35), residues: 209 loop : -0.50 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 211 TYR 0.005 0.001 TYR A 68 PHE 0.014 0.002 PHE E 141 TRP 0.018 0.001 TRP D 180 HIS 0.011 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (14511) covalent geometry : angle 0.46046 / 0.24 (19651) hydrogen bonds : bond 0.04521 / 3.01 ( 1002) hydrogen bonds : angle 3.60228 / 2.56 ( 2956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8519 (mtp85) cc_final: 0.7967 (mmm160) REVERT: A 77 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7126 (tp30) REVERT: A 202 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7270 (mp0) REVERT: A 261 ILE cc_start: 0.9453 (tp) cc_final: 0.9217 (tp) REVERT: C 40 GLU cc_start: 0.7981 (tp30) cc_final: 0.7746 (tp30) REVERT: C 184 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7977 (tpt-90) REVERT: C 281 GLU cc_start: 0.8694 (tt0) cc_final: 0.8486 (tt0) REVERT: B 21 THR cc_start: 0.8508 (m) cc_final: 0.8126 (p) REVERT: E 203 GLN cc_start: 0.8263 (tt0) cc_final: 0.7738 (tm-30) REVERT: E 205 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (mp) REVERT: D 103 GLU cc_start: 0.8088 (pt0) cc_final: 0.7695 (mt-10) REVERT: D 122 ASP cc_start: 0.7914 (t0) cc_final: 0.7563 (t70) REVERT: D 126 ILE cc_start: 0.5851 (tp) cc_final: 0.5539 (pt) REVERT: F 40 GLU cc_start: 0.8686 (tp30) cc_final: 0.8263 (tp30) REVERT: F 179 GLN cc_start: 0.7769 (mt0) cc_final: 0.7213 (tp-100) REVERT: F 271 GLU cc_start: 0.8538 (tp30) cc_final: 0.8069 (tp30) outliers start: 20 outliers final: 10 residues processed: 186 average time/residue: 0.1510 time to fit residues: 39.2746 Evaluate side-chains 182 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 6 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 145 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108511 restraints weight = 17663.358| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.29 r_work: 0.3130 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14511 Z= 0.143 Angle : 0.464 6.819 19651 Z= 0.241 Chirality : 0.035 0.158 2250 Planarity : 0.003 0.051 2500 Dihedral : 8.658 89.252 2165 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.21 % Allowed : 10.79 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.20), residues: 1700 helix: 2.90 (0.14), residues: 1124 sheet: 2.19 (0.35), residues: 209 loop : -0.53 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 211 TYR 0.005 0.001 TYR A 68 PHE 0.014 0.002 PHE E 141 TRP 0.019 0.001 TRP D 180 HIS 0.009 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14511) covalent geometry : angle 0.46352 / 0.24 (19651) hydrogen bonds : bond 0.04443 / 2.95 ( 1002) hydrogen bonds : angle 3.56596 / 2.54 ( 2956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7862 (mmm160) REVERT: A 77 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7080 (tp30) REVERT: A 202 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7178 (mp0) REVERT: A 261 ILE cc_start: 0.9446 (tp) cc_final: 0.9225 (tp) REVERT: C 40 GLU cc_start: 0.8010 (tp30) cc_final: 0.7757 (tp30) REVERT: C 111 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8407 (ttp-110) REVERT: C 184 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7818 (tpt-90) REVERT: C 281 GLU cc_start: 0.8661 (tt0) cc_final: 0.8418 (tt0) REVERT: B 21 THR cc_start: 0.8390 (m) cc_final: 0.8025 (p) REVERT: E 203 GLN cc_start: 0.8271 (tt0) cc_final: 0.7776 (tm-30) REVERT: E 205 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7806 (mp) REVERT: D 103 GLU cc_start: 0.8074 (pt0) cc_final: 0.7637 (mt-10) REVERT: D 122 ASP cc_start: 0.7935 (t0) cc_final: 0.7554 (t70) REVERT: D 126 ILE cc_start: 0.5601 (tp) cc_final: 0.5311 (pt) REVERT: F 40 GLU cc_start: 0.8735 (tp30) cc_final: 0.8266 (tp30) REVERT: F 179 GLN cc_start: 0.7726 (mt0) cc_final: 0.7163 (tp-100) REVERT: F 271 GLU cc_start: 0.8444 (tp30) cc_final: 0.7931 (tp30) outliers start: 18 outliers final: 10 residues processed: 184 average time/residue: 0.1580 time to fit residues: 40.4520 Evaluate side-chains 179 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106417 restraints weight = 17818.692| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.28 r_work: 0.3101 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14511 Z= 0.195 Angle : 0.504 6.850 19651 Z= 0.260 Chirality : 0.037 0.210 2250 Planarity : 0.003 0.033 2500 Dihedral : 8.694 87.584 2165 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 11.80 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.20), residues: 1700 helix: 2.81 (0.14), residues: 1122 sheet: 2.12 (0.35), residues: 209 loop : -0.49 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 59 TYR 0.006 0.001 TYR A 68 PHE 0.017 0.002 PHE E 141 TRP 0.023 0.001 TRP D 180 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (14511) covalent geometry : angle 0.50356 / 0.26 (19651) hydrogen bonds : bond 0.04745 / 3.16 ( 1002) hydrogen bonds : angle 3.64076 / 2.59 ( 2956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8482 (mtp85) cc_final: 0.7901 (mmm160) REVERT: A 77 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7103 (tp30) REVERT: A 202 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7218 (mp0) REVERT: A 261 ILE cc_start: 0.9463 (tp) cc_final: 0.9237 (tp) REVERT: C 40 GLU cc_start: 0.8038 (tp30) cc_final: 0.7798 (tp30) REVERT: C 81 ASN cc_start: 0.7704 (t0) cc_final: 0.7131 (t0) REVERT: C 111 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8384 (ttp-110) REVERT: C 184 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7875 (tpt-90) REVERT: C 281 GLU cc_start: 0.8691 (tt0) cc_final: 0.8448 (tt0) REVERT: B 21 THR cc_start: 0.8471 (m) cc_final: 0.8121 (p) REVERT: B 33 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 37 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8159 (mtp85) REVERT: E 203 GLN cc_start: 0.8309 (tt0) cc_final: 0.7818 (tm-30) REVERT: E 205 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7820 (mp) REVERT: D 121 GLN cc_start: 0.7283 (mp10) cc_final: 0.7059 (mp10) REVERT: D 122 ASP cc_start: 0.7979 (t0) cc_final: 0.7591 (t70) REVERT: D 126 ILE cc_start: 0.5444 (tp) cc_final: 0.5122 (pt) REVERT: F 40 GLU cc_start: 0.8724 (tp30) cc_final: 0.8341 (tp30) REVERT: F 271 GLU cc_start: 0.8479 (tp30) cc_final: 0.8161 (tp30) outliers start: 16 outliers final: 10 residues processed: 187 average time/residue: 0.1300 time to fit residues: 33.5184 Evaluate side-chains 185 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106271 restraints weight = 17793.047| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.28 r_work: 0.3099 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14511 Z= 0.195 Angle : 0.511 6.576 19651 Z= 0.264 Chirality : 0.037 0.201 2250 Planarity : 0.003 0.044 2500 Dihedral : 8.695 87.304 2165 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.94 % Allowed : 12.06 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.20), residues: 1700 helix: 2.77 (0.14), residues: 1122 sheet: 2.01 (0.35), residues: 210 loop : -0.53 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.006 0.001 TYR A 68 PHE 0.016 0.002 PHE E 141 TRP 0.026 0.001 TRP D 180 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.19 (14511) covalent geometry : angle 0.51143 / 0.26 (19651) hydrogen bonds : bond 0.04720 / 3.15 ( 1002) hydrogen bonds : angle 3.64996 / 2.60 ( 2956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8495 (mtp85) cc_final: 0.7938 (mmm160) REVERT: A 77 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7131 (tp30) REVERT: A 202 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7257 (mp0) REVERT: A 261 ILE cc_start: 0.9463 (tp) cc_final: 0.9231 (tp) REVERT: C 40 GLU cc_start: 0.7984 (tp30) cc_final: 0.7741 (tp30) REVERT: C 81 ASN cc_start: 0.7764 (t0) cc_final: 0.7151 (t0) REVERT: C 111 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8450 (ttp-110) REVERT: C 184 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7926 (tpt-90) REVERT: C 281 GLU cc_start: 0.8631 (tt0) cc_final: 0.8395 (tt0) REVERT: B 21 THR cc_start: 0.8473 (m) cc_final: 0.8132 (p) REVERT: B 33 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 37 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8184 (mtp85) REVERT: E 203 GLN cc_start: 0.8331 (tt0) cc_final: 0.7834 (tm-30) REVERT: E 205 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7872 (mp) REVERT: D 5 MET cc_start: 0.9091 (ttm) cc_final: 0.8856 (mtp) REVERT: D 121 GLN cc_start: 0.7329 (mp10) cc_final: 0.7125 (mp10) REVERT: D 122 ASP cc_start: 0.8010 (t0) cc_final: 0.7650 (t70) REVERT: D 126 ILE cc_start: 0.5545 (tp) cc_final: 0.5207 (pt) REVERT: F 40 GLU cc_start: 0.8732 (tp30) cc_final: 0.8347 (tp30) REVERT: F 271 GLU cc_start: 0.8497 (tp30) cc_final: 0.8188 (tp30) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 0.1506 time to fit residues: 38.1660 Evaluate side-chains 183 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109228 restraints weight = 17777.438| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.31 r_work: 0.3140 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14511 Z= 0.114 Angle : 0.472 7.497 19651 Z= 0.244 Chirality : 0.034 0.182 2250 Planarity : 0.003 0.044 2500 Dihedral : 8.706 88.469 2165 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.80 % Allowed : 12.27 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.20), residues: 1700 helix: 2.95 (0.14), residues: 1122 sheet: 2.03 (0.35), residues: 210 loop : -0.52 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 37 TYR 0.005 0.001 TYR A 68 PHE 0.013 0.001 PHE E 141 TRP 0.025 0.001 TRP D 180 HIS 0.031 0.002 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14511) covalent geometry : angle 0.47183 / 0.24 (19651) hydrogen bonds : bond 0.04251 / 2.83 ( 1002) hydrogen bonds : angle 3.51425 / 2.50 ( 2956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7851 (mmm160) REVERT: A 77 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7161 (tp30) REVERT: A 202 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7138 (mp0) REVERT: A 261 ILE cc_start: 0.9428 (tp) cc_final: 0.9206 (tp) REVERT: C 40 GLU cc_start: 0.7953 (tp30) cc_final: 0.7720 (tp30) REVERT: C 68 TYR cc_start: 0.9059 (t80) cc_final: 0.8857 (t80) REVERT: C 184 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7862 (tpt-90) REVERT: C 281 GLU cc_start: 0.8620 (tt0) cc_final: 0.8376 (tt0) REVERT: B 21 THR cc_start: 0.8426 (m) cc_final: 0.8118 (p) REVERT: B 33 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7922 (mp0) REVERT: B 37 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8216 (mtp85) REVERT: E 203 GLN cc_start: 0.8319 (tt0) cc_final: 0.7804 (tm-30) REVERT: E 205 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7864 (mp) REVERT: E 243 ASP cc_start: 0.8938 (t0) cc_final: 0.8570 (t0) REVERT: D 122 ASP cc_start: 0.7961 (t0) cc_final: 0.7600 (t70) REVERT: D 126 ILE cc_start: 0.5346 (tp) cc_final: 0.5050 (pt) REVERT: F 40 GLU cc_start: 0.8707 (tp30) cc_final: 0.8249 (tp30) REVERT: F 271 GLU cc_start: 0.8460 (tp30) cc_final: 0.8127 (tp30) outliers start: 12 outliers final: 10 residues processed: 188 average time/residue: 0.1528 time to fit residues: 40.1005 Evaluate side-chains 183 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107981 restraints weight = 17780.275| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.31 r_work: 0.3123 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14511 Z= 0.154 Angle : 0.488 7.843 19651 Z= 0.251 Chirality : 0.036 0.177 2250 Planarity : 0.003 0.033 2500 Dihedral : 8.705 87.576 2165 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.67 % Allowed : 12.94 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.20), residues: 1700 helix: 2.89 (0.14), residues: 1122 sheet: 2.01 (0.35), residues: 210 loop : -0.53 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 111 TYR 0.006 0.001 TYR A 68 PHE 0.015 0.002 PHE E 141 TRP 0.027 0.001 TRP D 180 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (14511) covalent geometry : angle 0.48804 / 0.25 (19651) hydrogen bonds : bond 0.04368 / 2.92 ( 1002) hydrogen bonds : angle 3.53704 / 2.52 ( 2956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.28 seconds wall clock time: 57 minutes 21.25 seconds (3441.25 seconds total)