Starting phenix.real_space_refine on Fri Jul 3 11:56:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ves_43173/07_2026/8ves_43173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ves_43173/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ves_43173/07_2026/8ves_43173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ves_43173/07_2026/8ves_43173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ves_43173/07_2026/8ves_43173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ves_43173/07_2026/8ves_43173.map" } 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-dev-6108/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: 2.88, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 620.6 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: 1.18 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: 2.08 Time building geometry restraints manager: 1.53 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: 19276 1.05 - 2.11: 307 2.11 - 3.16: 47 3.16 - 4.21: 7 4.21 - 5.26: 14 Bond angle restraints: 19651 Sorted by residual: 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=" C1' U H 14 " pdb=" N1 U H 14 " pdb=" C6 U H 14 " ideal model delta sigma weight residual 121.20 117.75 3.45 1.40e+00 5.10e-01 6.06e+00 angle pdb=" N1 U H 14 " pdb=" C6 U H 14 " pdb=" C5 U H 14 " ideal model delta sigma weight residual 122.70 123.85 -1.15 5.00e-01 4.00e+00 5.30e+00 angle pdb=" C ASN C 199 " pdb=" N ARG C 200 " pdb=" CA ARG C 200 " ideal model delta sigma weight residual 121.54 125.62 -4.08 1.91e+00 2.74e-01 4.56e+00 angle pdb=" N3 U H 14 " pdb=" C4 U H 14 " pdb=" O4 U H 14 " ideal model delta sigma weight residual 119.40 120.83 -1.43 7.00e-01 2.04e+00 4.14e+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: 1638 0.033 - 0.066: 494 0.066 - 0.099: 75 0.099 - 0.131: 41 0.131 - 0.164: 2 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=" CA VAL C 27 " pdb=" N VAL C 27 " pdb=" C VAL C 27 " pdb=" CB VAL C 27 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 27 " pdb=" N VAL D 27 " pdb=" C VAL D 27 " pdb=" CB VAL D 27 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-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: 0.560 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.420 Find NCS groups from input model: 0.280 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- 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= 0.141 Angle : 0.377 5.263 19651 Z= 0.214 Chirality : 0.034 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 0.00327 / 0.14 (14511) covalent geometry : angle 0.37736 / 0.21 (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 : 0.546 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: 0.1386 time to fit residues: 62.0988 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 : 0.436 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.144167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108063 restraints weight = 17695.654| |-----------------------------------------------------------------------------| 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: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14511 Z= 0.162 Angle : 0.508 6.005 19651 Z= 0.277 Chirality : 0.036 0.136 2250 Planarity : 0.004 0.067 2500 Dihedral : 8.812 95.468 2165 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.01 % Allowed : 5.56 % Favored : 93.43 % 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: 2.93 (0.20), residues: 1700 helix: 2.58 (0.14), residues: 1121 sheet: 2.43 (0.37), residues: 199 loop : -0.39 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 10 TYR 0.007 0.001 TYR A 68 PHE 0.015 0.002 PHE E 141 TRP 0.009 0.001 TRP F 94 HIS 0.005 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (14511) covalent geometry : angle 0.50777 / 0.28 (19651) hydrogen bonds : bond 0.06143 / 4.09 ( 1002) hydrogen bonds : angle 4.08529 / 2.91 ( 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 225 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: A 67 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8035 (mmm160) REVERT: A 77 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7144 (tp30) REVERT: A 202 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7338 (mp0) REVERT: C 40 GLU cc_start: 0.7989 (tp30) cc_final: 0.7752 (tp30) REVERT: C 174 MET cc_start: 0.8357 (tpp) cc_final: 0.7930 (mmm) REVERT: C 184 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.7934 (tpt-90) REVERT: C 279 MET cc_start: 0.8826 (ttm) cc_final: 0.8545 (mtm) REVERT: C 281 GLU cc_start: 0.8663 (tt0) cc_final: 0.8278 (tt0) REVERT: B 69 GLU cc_start: 0.8149 (tt0) cc_final: 0.7927 (tt0) REVERT: B 219 ASP cc_start: 0.8410 (t0) cc_final: 0.8182 (t0) REVERT: B 246 MET cc_start: 0.8573 (mmm) cc_final: 0.7746 (mmp) REVERT: E 201 LEU cc_start: 0.7827 (tp) cc_final: 0.7554 (tp) REVERT: E 202 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 205 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7265 (mp) REVERT: E 243 ASP cc_start: 0.9056 (t0) cc_final: 0.8707 (t0) REVERT: D 122 ASP cc_start: 0.8071 (t0) cc_final: 0.7806 (t70) REVERT: F 21 THR cc_start: 0.9114 (m) cc_final: 0.8877 (p) REVERT: F 40 GLU cc_start: 0.8663 (tp30) cc_final: 0.8239 (tp30) REVERT: F 174 MET cc_start: 0.7843 (tpt) cc_final: 0.7284 (tpt) REVERT: F 179 GLN cc_start: 0.7698 (mt0) cc_final: 0.7192 (tp-100) REVERT: F 271 GLU cc_start: 0.8530 (tp30) cc_final: 0.8056 (tp30) outliers start: 15 outliers final: 7 residues processed: 219 average time/residue: 0.1358 time to fit residues: 41.4646 Evaluate side-chains 183 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 205 LEU 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: 5.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109770 restraints weight = 17756.063| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.30 r_work: 0.3156 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14511 Z= 0.124 Angle : 0.459 9.524 19651 Z= 0.243 Chirality : 0.035 0.193 2250 Planarity : 0.003 0.025 2500 Dihedral : 8.678 94.648 2165 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.01 % Allowed : 7.17 % Favored : 91.82 % 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: 3.15 (0.20), residues: 1700 helix: 2.80 (0.14), residues: 1121 sheet: 2.35 (0.36), residues: 203 loop : -0.44 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 37 TYR 0.005 0.001 TYR A 68 PHE 0.013 0.001 PHE E 141 TRP 0.012 0.001 TRP E 180 HIS 0.009 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14511) covalent geometry : angle 0.45919 / 0.24 (19651) hydrogen bonds : bond 0.05104 / 3.40 ( 1002) hydrogen bonds : angle 3.80331 / 2.70 ( 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: 15 poor density : 186 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8001 (mmm160) REVERT: A 77 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7144 (tp30) REVERT: A 202 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7355 (mp0) REVERT: A 227 GLU cc_start: 0.8240 (tp30) cc_final: 0.7702 (tt0) REVERT: A 246 MET cc_start: 0.8781 (mmt) cc_final: 0.8500 (mmt) REVERT: C 40 GLU cc_start: 0.7968 (tp30) cc_final: 0.7711 (tp30) REVERT: C 174 MET cc_start: 0.8219 (tpp) cc_final: 0.7863 (mmm) REVERT: C 184 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7905 (tpt-90) REVERT: C 246 MET cc_start: 0.8842 (mmp) cc_final: 0.8038 (mmp) REVERT: C 281 GLU cc_start: 0.8654 (tt0) cc_final: 0.8425 (tt0) REVERT: B 69 GLU cc_start: 0.8212 (tt0) cc_final: 0.8009 (tt0) REVERT: E 203 GLN cc_start: 0.8160 (tt0) cc_final: 0.7599 (tm-30) REVERT: D 122 ASP cc_start: 0.7973 (t0) cc_final: 0.7664 (t70) REVERT: F 40 GLU cc_start: 0.8644 (tp30) cc_final: 0.8221 (tp30) REVERT: F 174 MET cc_start: 0.7717 (tpt) cc_final: 0.7356 (tpt) REVERT: F 176 GLU cc_start: 0.7912 (tp30) cc_final: 0.7687 (tp30) REVERT: F 179 GLN cc_start: 0.7658 (mt0) cc_final: 0.7160 (tp-100) REVERT: F 271 GLU cc_start: 0.8522 (tp30) cc_final: 0.8054 (tp30) outliers start: 15 outliers final: 7 residues processed: 197 average time/residue: 0.1328 time to fit residues: 36.5076 Evaluate side-chains 185 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP 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 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: 0.8980 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: 0.9990 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109276 restraints weight = 17786.458| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.28 r_work: 0.3158 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14511 Z= 0.134 Angle : 0.457 6.797 19651 Z= 0.240 Chirality : 0.035 0.171 2250 Planarity : 0.003 0.026 2500 Dihedral : 8.650 93.533 2165 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.80 % Allowed : 9.25 % Favored : 89.95 % 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: 3.21 (0.20), residues: 1700 helix: 2.87 (0.14), residues: 1123 sheet: 2.25 (0.35), residues: 209 loop : -0.44 (0.31), residues: 368 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 0.014 0.002 PHE E 141 TRP 0.015 0.001 TRP E 180 HIS 0.005 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14511) covalent geometry : angle 0.45720 / 0.24 (19651) hydrogen bonds : bond 0.04708 / 3.13 ( 1002) hydrogen bonds : angle 3.70647 / 2.64 ( 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 199 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8030 (mmm160) REVERT: A 77 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7154 (tp30) REVERT: A 202 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 246 MET cc_start: 0.8786 (mmt) cc_final: 0.8429 (mmt) REVERT: C 24 MET cc_start: 0.8860 (mtp) cc_final: 0.8656 (mtm) REVERT: C 40 GLU cc_start: 0.8003 (tp30) cc_final: 0.7748 (tp30) REVERT: C 174 MET cc_start: 0.8268 (tpp) cc_final: 0.7924 (mmm) REVERT: C 184 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.7983 (tpt-90) REVERT: C 246 MET cc_start: 0.8960 (mmp) cc_final: 0.8421 (mmp) REVERT: C 281 GLU cc_start: 0.8711 (tt0) cc_final: 0.8370 (tt0) REVERT: B 63 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 69 GLU cc_start: 0.8198 (tt0) cc_final: 0.7971 (tt0) REVERT: B 285 ASN cc_start: 0.8686 (t0) cc_final: 0.8460 (t0) REVERT: E 203 GLN cc_start: 0.8222 (tt0) cc_final: 0.7632 (tm-30) REVERT: E 243 ASP cc_start: 0.9011 (t0) cc_final: 0.8626 (t0) REVERT: D 122 ASP cc_start: 0.7951 (t0) cc_final: 0.7556 (t70) REVERT: D 126 ILE cc_start: 0.5826 (tp) cc_final: 0.5467 (pt) REVERT: F 40 GLU cc_start: 0.8671 (tp30) cc_final: 0.8247 (tp30) REVERT: F 174 MET cc_start: 0.7750 (tpt) cc_final: 0.7486 (tpt) REVERT: F 176 GLU cc_start: 0.7903 (tp30) cc_final: 0.7648 (tp30) REVERT: F 179 GLN cc_start: 0.7742 (mt0) cc_final: 0.7252 (tp-100) REVERT: F 271 GLU cc_start: 0.8537 (tp30) cc_final: 0.8076 (tp30) outliers start: 12 outliers final: 7 residues processed: 194 average time/residue: 0.1458 time to fit residues: 39.5465 Evaluate side-chains 174 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 MET Chi-restraints excluded: chain B residue 147 THR 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: 6.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.143059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106949 restraints weight = 17866.999| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.30 r_work: 0.3111 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2141 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= 0.175 Angle : 0.477 7.660 19651 Z= 0.250 Chirality : 0.036 0.145 2250 Planarity : 0.003 0.039 2500 Dihedral : 8.629 92.042 2165 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.01 % Allowed : 9.79 % 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: 3.13 (0.20), residues: 1700 helix: 2.82 (0.14), residues: 1126 sheet: 2.18 (0.35), residues: 202 loop : -0.50 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.007 0.001 TYR A 68 PHE 0.016 0.002 PHE E 141 TRP 0.015 0.001 TRP E 180 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (14511) covalent geometry : angle 0.47671 / 0.25 (19651) hydrogen bonds : bond 0.04770 / 3.17 ( 1002) hydrogen bonds : angle 3.69265 / 2.63 ( 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 188 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7939 (mmm160) REVERT: A 77 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7100 (tp30) REVERT: A 202 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7253 (mp0) REVERT: A 261 ILE cc_start: 0.9463 (tp) cc_final: 0.9241 (tp) REVERT: C 40 GLU cc_start: 0.8000 (tp30) cc_final: 0.7757 (tp30) REVERT: C 174 MET cc_start: 0.8203 (tpp) cc_final: 0.7851 (mmm) REVERT: C 184 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7899 (tpt-90) REVERT: C 246 MET cc_start: 0.8970 (mmp) cc_final: 0.8557 (mmp) REVERT: C 281 GLU cc_start: 0.8681 (tt0) cc_final: 0.8443 (tt0) REVERT: B 69 GLU cc_start: 0.8177 (tt0) cc_final: 0.7949 (tt0) REVERT: E 203 GLN cc_start: 0.8228 (tt0) cc_final: 0.7731 (tm-30) REVERT: E 205 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 103 GLU cc_start: 0.8081 (pt0) cc_final: 0.7822 (mt-10) REVERT: D 122 ASP cc_start: 0.7978 (t0) cc_final: 0.7581 (t70) REVERT: D 126 ILE cc_start: 0.5777 (tp) cc_final: 0.5431 (pt) REVERT: F 40 GLU cc_start: 0.8719 (tp30) cc_final: 0.8274 (tp30) REVERT: F 179 GLN cc_start: 0.7731 (mt0) cc_final: 0.7155 (tp-100) REVERT: F 271 GLU cc_start: 0.8496 (tp30) cc_final: 0.8000 (tp30) outliers start: 15 outliers final: 5 residues processed: 183 average time/residue: 0.1442 time to fit residues: 36.8291 Evaluate side-chains 175 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109198 restraints weight = 17728.396| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.29 r_work: 0.3156 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2281 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= 0.122 Angle : 0.442 7.316 19651 Z= 0.232 Chirality : 0.034 0.165 2250 Planarity : 0.003 0.031 2500 Dihedral : 8.611 92.642 2165 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.07 % Allowed : 10.19 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.20), residues: 1700 helix: 2.97 (0.14), residues: 1121 sheet: 2.16 (0.35), residues: 209 loop : -0.50 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 37 TYR 0.005 0.001 TYR A 68 PHE 0.013 0.001 PHE E 141 TRP 0.016 0.001 TRP E 180 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14511) covalent geometry : angle 0.44160 / 0.23 (19651) hydrogen bonds : bond 0.04345 / 2.89 ( 1002) hydrogen bonds : angle 3.56084 / 2.53 ( 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 197 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8527 (mtp85) cc_final: 0.7973 (mmm160) REVERT: A 77 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7138 (tp30) REVERT: A 202 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7280 (mp0) REVERT: A 261 ILE cc_start: 0.9438 (tp) cc_final: 0.9200 (tp) REVERT: C 40 GLU cc_start: 0.8031 (tp30) cc_final: 0.7812 (tp30) REVERT: C 184 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.8003 (tpt-90) REVERT: C 246 MET cc_start: 0.9000 (mmp) cc_final: 0.8750 (mmp) REVERT: C 281 GLU cc_start: 0.8627 (tt0) cc_final: 0.8408 (tt0) REVERT: B 21 THR cc_start: 0.8484 (m) cc_final: 0.8119 (p) REVERT: B 285 ASN cc_start: 0.8670 (t0) cc_final: 0.8453 (t0) REVERT: E 203 GLN cc_start: 0.8286 (tt0) cc_final: 0.7811 (tm-30) REVERT: E 205 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 103 GLU cc_start: 0.8102 (pt0) cc_final: 0.7685 (mt-10) REVERT: D 122 ASP cc_start: 0.7895 (t0) cc_final: 0.7538 (t70) REVERT: D 126 ILE cc_start: 0.5845 (tp) cc_final: 0.5548 (pt) REVERT: D 180 TRP cc_start: 0.7693 (t60) cc_final: 0.7458 (t60) REVERT: F 40 GLU cc_start: 0.8685 (tp30) cc_final: 0.8250 (tp30) REVERT: F 179 GLN cc_start: 0.7742 (mt0) cc_final: 0.7198 (tp-100) REVERT: F 271 GLU cc_start: 0.8533 (tp30) cc_final: 0.8222 (tp30) outliers start: 16 outliers final: 8 residues processed: 194 average time/residue: 0.1519 time to fit residues: 41.0013 Evaluate side-chains 181 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP 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 D residue 272 LEU 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=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: 0.9990 chunk 89 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.144167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108345 restraints weight = 17665.897| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.28 r_work: 0.3143 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14511 Z= 0.147 Angle : 0.462 7.073 19651 Z= 0.240 Chirality : 0.035 0.167 2250 Planarity : 0.003 0.037 2500 Dihedral : 8.641 91.490 2165 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.01 % Allowed : 10.72 % Favored : 88.27 % 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: 3.26 (0.20), residues: 1700 helix: 2.94 (0.14), residues: 1124 sheet: 2.13 (0.35), residues: 208 loop : -0.48 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 111 TYR 0.008 0.001 TYR C 68 PHE 0.014 0.002 PHE E 141 TRP 0.016 0.001 TRP E 180 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14511) covalent geometry : angle 0.46161 / 0.24 (19651) hydrogen bonds : bond 0.04400 / 2.92 ( 1002) hydrogen bonds : angle 3.55559 / 2.53 ( 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 187 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8170 (tpp80) REVERT: A 67 ARG cc_start: 0.8522 (mtp85) cc_final: 0.7974 (mmm160) REVERT: A 77 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7211 (tp30) REVERT: A 202 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7262 (mp0) REVERT: A 261 ILE cc_start: 0.9439 (tp) cc_final: 0.9203 (tp) REVERT: C 40 GLU cc_start: 0.8045 (tp30) cc_final: 0.7822 (tp30) REVERT: C 184 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7957 (tpt-90) REVERT: C 281 GLU cc_start: 0.8674 (tt0) cc_final: 0.8469 (tt0) REVERT: B 21 THR cc_start: 0.8539 (m) cc_final: 0.8185 (p) REVERT: B 33 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7993 (mp0) REVERT: B 285 ASN cc_start: 0.8685 (t0) cc_final: 0.8474 (t0) REVERT: E 203 GLN cc_start: 0.8306 (tt0) cc_final: 0.7817 (tm-30) REVERT: E 205 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7993 (mp) REVERT: D 103 GLU cc_start: 0.8124 (pt0) cc_final: 0.7714 (mt-10) REVERT: D 122 ASP cc_start: 0.7877 (t0) cc_final: 0.7543 (t70) REVERT: D 126 ILE cc_start: 0.5588 (tp) cc_final: 0.5271 (pt) REVERT: D 180 TRP cc_start: 0.7685 (t60) cc_final: 0.7463 (t60) REVERT: F 40 GLU cc_start: 0.8675 (tp30) cc_final: 0.8245 (tp30) REVERT: F 271 GLU cc_start: 0.8547 (tp30) cc_final: 0.8083 (tp30) outliers start: 15 outliers final: 10 residues processed: 184 average time/residue: 0.1426 time to fit residues: 36.7224 Evaluate side-chains 181 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 THR Chi-restraints excluded: chain B 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 Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.143286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109339 restraints weight = 17535.650| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.15 r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14511 Z= 0.132 Angle : 0.457 7.067 19651 Z= 0.237 Chirality : 0.035 0.150 2250 Planarity : 0.003 0.036 2500 Dihedral : 8.647 91.495 2165 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.01 % Allowed : 11.13 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.20), residues: 1700 helix: 2.97 (0.14), residues: 1122 sheet: 2.15 (0.35), residues: 209 loop : -0.44 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 37 TYR 0.007 0.001 TYR C 68 PHE 0.014 0.002 PHE E 141 TRP 0.016 0.001 TRP E 180 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14511) covalent geometry : angle 0.45708 / 0.24 (19651) hydrogen bonds : bond 0.04300 / 2.86 ( 1002) hydrogen bonds : angle 3.52830 / 2.52 ( 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 188 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7854 (mmm160) REVERT: A 77 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7150 (tp30) REVERT: A 202 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7138 (mp0) REVERT: A 261 ILE cc_start: 0.9432 (tp) cc_final: 0.9208 (tp) REVERT: C 40 GLU cc_start: 0.8026 (tp30) cc_final: 0.7785 (tp30) REVERT: C 184 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7822 (tpt-90) REVERT: C 281 GLU cc_start: 0.8587 (tt0) cc_final: 0.8336 (tt0) REVERT: B 21 THR cc_start: 0.8422 (m) cc_final: 0.8071 (p) REVERT: B 33 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7934 (mp0) REVERT: B 285 ASN cc_start: 0.8605 (t0) cc_final: 0.8387 (t0) REVERT: E 203 GLN cc_start: 0.8294 (tt0) cc_final: 0.7779 (tm-30) REVERT: E 205 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7861 (mp) REVERT: D 122 ASP cc_start: 0.7883 (t0) cc_final: 0.7526 (t70) REVERT: D 126 ILE cc_start: 0.5302 (tp) cc_final: 0.5003 (pt) REVERT: D 180 TRP cc_start: 0.7617 (t60) cc_final: 0.7401 (t60) REVERT: F 40 GLU cc_start: 0.8704 (tp30) cc_final: 0.8233 (tp30) REVERT: F 271 GLU cc_start: 0.8423 (tp30) cc_final: 0.7908 (tp30) outliers start: 15 outliers final: 11 residues processed: 184 average time/residue: 0.1409 time to fit residues: 36.6747 Evaluate side-chains 182 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 THR Chi-restraints excluded: chain B residue 211 ARG 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 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: 7.9990 chunk 19 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.141112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104915 restraints weight = 17859.491| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.32 r_work: 0.3082 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14511 Z= 0.246 Angle : 0.545 7.634 19651 Z= 0.281 Chirality : 0.038 0.159 2250 Planarity : 0.004 0.049 2500 Dihedral : 8.739 88.824 2165 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.07 % Allowed : 11.60 % Favored : 87.33 % 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: 2.99 (0.20), residues: 1700 helix: 2.74 (0.15), residues: 1121 sheet: 2.03 (0.36), residues: 202 loop : -0.56 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 211 TYR 0.009 0.001 TYR C 68 PHE 0.018 0.003 PHE C 249 TRP 0.017 0.001 TRP E 180 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (14511) covalent geometry : angle 0.54495 / 0.28 (19651) hydrogen bonds : bond 0.04995 / 3.33 ( 1002) hydrogen bonds : angle 3.70048 / 2.64 ( 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 186 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7981 (mmm160) REVERT: A 202 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7289 (mp0) REVERT: A 261 ILE cc_start: 0.9458 (tp) cc_final: 0.9218 (tp) REVERT: C 40 GLU cc_start: 0.8015 (tp30) cc_final: 0.7779 (tp30) REVERT: C 81 ASN cc_start: 0.7860 (t0) cc_final: 0.7301 (t0) REVERT: C 184 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.7957 (tpt-90) REVERT: C 281 GLU cc_start: 0.8646 (tt0) cc_final: 0.8422 (tt0) REVERT: B 21 THR cc_start: 0.8565 (m) cc_final: 0.8223 (p) REVERT: B 33 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8052 (mp0) REVERT: E 203 GLN cc_start: 0.8340 (tt0) cc_final: 0.7851 (tm-30) REVERT: D 122 ASP cc_start: 0.7981 (t0) cc_final: 0.7640 (t70) REVERT: D 126 ILE cc_start: 0.5645 (tp) cc_final: 0.5290 (pt) REVERT: F 40 GLU cc_start: 0.8689 (tp30) cc_final: 0.8325 (tp30) REVERT: F 271 GLU cc_start: 0.8546 (tp30) cc_final: 0.8062 (tp30) outliers start: 16 outliers final: 10 residues processed: 180 average time/residue: 0.1558 time to fit residues: 38.8493 Evaluate side-chains 175 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 97 MET 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 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 38 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.143211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107313 restraints weight = 17822.451| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.29 r_work: 0.3117 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14511 Z= 0.150 Angle : 0.501 7.560 19651 Z= 0.258 Chirality : 0.035 0.148 2250 Planarity : 0.003 0.061 2500 Dihedral : 8.726 90.159 2165 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.54 % Allowed : 12.20 % Favored : 87.27 % 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: 2.84 (0.14), residues: 1122 sheet: 1.98 (0.35), residues: 210 loop : -0.51 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 211 TYR 0.006 0.001 TYR C 68 PHE 0.015 0.002 PHE E 141 TRP 0.019 0.001 TRP E 180 HIS 0.018 0.002 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (14511) covalent geometry : angle 0.50146 / 0.26 (19651) hydrogen bonds : bond 0.04567 / 3.03 ( 1002) hydrogen bonds : angle 3.60428 / 2.57 ( 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 175 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7884 (mmm160) REVERT: A 77 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7103 (tp30) REVERT: A 202 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7180 (mp0) REVERT: A 246 MET cc_start: 0.8815 (mmt) cc_final: 0.8203 (mmt) REVERT: A 261 ILE cc_start: 0.9446 (tp) cc_final: 0.9218 (tp) REVERT: C 40 GLU cc_start: 0.7988 (tp30) cc_final: 0.7750 (tp30) REVERT: C 184 ARG cc_start: 0.8169 (tpp-160) cc_final: 0.7873 (tpt-90) REVERT: C 281 GLU cc_start: 0.8637 (tt0) cc_final: 0.8398 (tt0) REVERT: B 21 THR cc_start: 0.8474 (m) cc_final: 0.8151 (p) REVERT: B 33 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7984 (mp0) REVERT: E 203 GLN cc_start: 0.8266 (tt0) cc_final: 0.7822 (tm-30) REVERT: D 5 MET cc_start: 0.9103 (ttm) cc_final: 0.8886 (mtp) REVERT: D 122 ASP cc_start: 0.7964 (t0) cc_final: 0.7622 (t70) REVERT: D 126 ILE cc_start: 0.5412 (tp) cc_final: 0.5090 (pt) REVERT: F 40 GLU cc_start: 0.8734 (tp30) cc_final: 0.8340 (tp30) REVERT: F 271 GLU cc_start: 0.8476 (tp30) cc_final: 0.8157 (tp30) outliers start: 8 outliers final: 7 residues processed: 173 average time/residue: 0.1542 time to fit residues: 36.7527 Evaluate side-chains 171 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 147 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.145188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109358 restraints weight = 17685.440| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.32 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14511 Z= 0.120 Angle : 0.477 7.695 19651 Z= 0.244 Chirality : 0.034 0.137 2250 Planarity : 0.003 0.061 2500 Dihedral : 8.719 90.778 2165 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.60 % Allowed : 12.40 % 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: 3.27 (0.20), residues: 1700 helix: 2.99 (0.14), residues: 1122 sheet: 1.98 (0.35), residues: 210 loop : -0.51 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 211 TYR 0.006 0.001 TYR C 68 PHE 0.014 0.001 PHE E 141 TRP 0.019 0.001 TRP E 180 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14511) covalent geometry : angle 0.47675 / 0.24 (19651) hydrogen bonds : bond 0.04115 / 2.74 ( 1002) hydrogen bonds : angle 3.49579 / 2.49 ( 2956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.51 seconds wall clock time: 59 minutes 54.37 seconds (3594.37 seconds total)